Human Proteome Organization (HUPO) News

Have you recently published an original article on proteomics research?

Fri, 27 Mar 2026 15:23:29 GMT

The HUPO Early Career Researcher (ECR) Committee warmly encourages eligible researchers to submit their recent publications to the HUPO ECR Manuscript Competition, sponsored by Taylor & Francis, for the opportunity to present at HUPO 2026 in Singapore. The competition celebrates the contributions of early career scientists and offers a global stage to highlight their work.

Early career researchers — including postdoctoral fellows, young clinicians, and junior faculty — with a manuscript published or accepted in 2025 or 2026 are encouraged to apply. Three finalists will be invited to present their research at HUPO 2026, where an expert committee will select the “Proteomics Highlight of the Year.”

Eligibility criteria: This competition is intended for:

Postdoctoral fellows (Ph.D. degree awarded post January 2020),
Junior faculty members (appointment post January 2022 and PhD awarded post January 2014), and
Young clinicians (M.D. degree awarded post January 2019).
Applicants must be HUPO members.
Career interruptions and leave, such as parental leave, will be considered to extend the eligibility period.
Finalists from previous years are not eligible to participate.

Publication criteria:

The applicant must have contributed significantly to the publication as the first or last (or shared first/last) author.
The publication must be an original research article.
Review articles will not be considered for this competition.
The publication must have been accepted or printed for publication at the time of submission for the competition, but must not have been published before January 1, 2025.
Manuscripts that were posted on bioRxiv and other pre-print servers prior to publication will be considered (i.e., prior to January 1, 2025).
The publication must be written in English.

How to Apply: A complete application must include the documents listed below. Send completed applications by email to ecr@hupo.org.

Single publication file as a pdf (including the supplementary information if applicable)
A short statement (300 words maximum) in which the applicant describes the novelty and impact of the publication on the field of proteomics.
Evidence of HUPO membership (e.g. screenshot of HUPO membership or member ID)

Prize: Awards will be presented during the Closing Ceremony & Awards Session at HUPO 2026. Cash prizes (USD 1,000 to the winner and USD 500 each to two runners-up) will be provided after the Congress.

HUPOST February 2026

Fri, 27 Feb 2026 18:24:54 GMT

The HUPOST February 2026 issue is here!

Featuring: Congress Updates, ECR News, ETC Highlights, HPP Developments & More

HUPOST February 2026: https://conta.cc/4cLAYAz

Submit your abstract and participate in the Poster Competition at HUPO 2026 in Singapore!

Wed, 25 Feb 2026 15:21:07 GMT

The HUPO Early Career Researcher (ECR) Committee is excited to present this year’s Poster Competition sponsored by Pelago Bioscience.

All graduate students (Master’s and PhD), as well as postdoctoral researchers, are invited to participate in the HUPO 2026 poster competition taking place on September 27 - October 1, 2026 in Singapore.

To participate, graduate students and postdocs simply need to indicate in their abstract submission that they would like to participate in the competition. This can be done by clicking the appropriate box while completing your submission. Posters in each trainee category (graduate students and postdocs) will be pre-selected based on quality, novelty, and potential impact of their abstracts. The authors of selected posters will be notified prior to the conference. Cash prizes of $500 will be awarded to the winner and $300 to two runners-up.

All early career proteomics researchers are invited to participate!

Best of luck to all!

Proudly sponsored by: Pelago Bioscience

Overview and Evaluation of the HUPO 2025 ETC Pre-Congress Training Sessions

Mon, 23 Feb 2026 22:38:47 GMT

At HUPO 2025, the HUPO Education and Training Committee (ETC) delivered three pre-congress training sessions, each organized and chaired by internationally recognized experts and designed to address different but complementary aspects of modern proteomics.

Session1: Exploring Protein Post-Translational Modifications (PTMs)

This session introduced contemporary strategies for studying protein post-translational modifications, with an emphasis on practical workflows, clinical sample preparation, and emerging directions in PTM and glycoproteomics research. Dr. Hu Zhou (Shanghai Institute of Materia Medica, CAS, China) provides in-depth guidance on PTMomics sample preparation, with a strong focus on practical considerations and best practices for clinical tumor samples. Dr. Nick Riley (University of Washington, USA) walks participants through a comprehensive glycoproteomics workflow and outlines emerging directions in glycoproteomics research. Together, the session highlights modern mass spectrometry–based strategies, key technical challenges, and future opportunities in PTM-focused proteomics, equipping students with actionable knowledge and a broader perspective on PTM biology and disease mechanisms. The session was chaired by Dr. Shixia Huang (Baylor College of Medicine) and Dr. Yansheng Liu (Yale University).

Session 2: Mastering Computational Proteomics

The three talks collectively emphasized that although proteomics now produces vast amounts of LC–MS/MS data, its full potential—particularly for experiment planning and AI-driven discovery—remains restricted by inconsistent metadata and technical variability across datasets. Dr. Deepti Jaiswal Kundu (EMBL-EBI) highlighted how standards such as the Sample and Data Relationship Format (SDRF) enable datasets to become machine-readable and reproducible, helping transform repositories like PRIDE and MassIVE from passive archives into genuinely reusable scientific resources. Dr. Tine Claeys (VIB-UGent Center for Medical Biotechnology) reinforced this message from an AI perspective, showing that meaningful, consistent annotation is essential for training reliable models such as MLMarker, and revealing how missing information, batch effects, and format inconsistencies silently undermine large-scale data reuse. Dr. Brian Searle (Mayo Clinic, USA) then demonstrated how deep learning tools such as Prosit can harmonize fragmented datasets into a shared coordinate framework, enabling the training of more generalizable models and unlocking the value of legacy experiments. Together, the talks made a compelling case that rigorous metadata standards and data harmonization are fundamental to robust data reuse and biologically meaningful AI in proteomics. The session was chaired by Dr. Deepti Jaiswal Kundu (EMBL-EBI, UK) and Dr. Giuseppe Palmisano (University of São Paulo, Brazil)

Session 3: Single-Cell Proteomics - Emerging Technologies and Translational Applications

The three talks collectively emphasized that single-cell proteomics is rapidly becoming a practical engine for resolving cellular heterogeneity and enabling precision medicine, driven by parallel advances in sample preparation, mass spectrometry, and computational analysis. Dr. Claudia Ctortecka (Broad Institute, USA) underscored that “precision starts with preparation,” walking through experimental design, randomization, QC, and workflow automation—highlighting ultra-sensitive acquisition strategies (including timsTOF Ultra2) that can quantify thousands of proteins per single cell and extend to low-cell-count tissue regions. Dr. Olga Vitek (Northeastern University, USA) reinforced that translation depends on robust statistics: she dissected how biological/technical variation, unbalanced designs, and uncertain cell-type labels can mislead differential analysis and provided practical recommendations for cell-type annotation and modeling choices that improve accuracy. Dr. Ana Konvalinka (University Health Network/University of Toronto, Canada) then connected these capabilities to clinical impact, illustrating how single-cell, tissue, and spatial proteomics can illuminate immune–parenchymal interactions, explain disease heterogeneity, and inform precision monitoring and future trial design. Together, the session made a clear case that scalable, reproducible end-to-end workflows spanning careful sample handling, appropriate statistical inference, and clinically grounded interpretation are essential for bringing single-cell proteomics into real-world translational and clinical use. The session was co-chaired by Dr. Ana Konvalinka (University Health Network/University of Toronto, Canada) and Dr. Lin Qingsong (National University of Singapore).

Summary of Participant Survey Results

Overall Summary

A total of 46 participants completed the post-congress survey across the three HUPO 2025 ETC pre-congress training sessions. Overall feedback was highly positive, with the large majority of respondents indicating that they would recommend the sessions to colleagues (40/46 Agree or Strongly Agree) and that they were interested in attending future HUPO ETC training events (40/46 Agree or Strongly Agree). Participants consistently valued the balance of conceptual grounding and practical insight, particularly where sessions addressed real-world challenges in experimental design, data interpretation, and emerging technologies. Qualitative comments emphasized the importance of expert-led instruction, clear workflows, and training that directly supports reproducibility and data reuse in proteomics research.

Session-Specific Survey Results

Exploring Protein Post-Translational Modifications (PTMs):

12 respondents completed the survey for this session. Feedback was uniformly positive, with respondents highlighting the practical guidance on PTMomics sample preparation, especially for clinical tumor specimens, and the clear, end-to-end overview of glycoproteomics workflows. Participants particularly valued the combination of hands-on considerations with forward-looking perspectives on PTM biology and disease mechanisms. Interest in future HUPO ETC training was very strong among this group, reflecting demand for structured, student-focused PTM education.

Mastering Computational Proteomics:

A total of 26 respondents identified this session (including minor duplicate session labels). Participants consistently emphasized the importance of metadata standards, data harmonization, and reproducibility as key take-home messages. Respondents noted that the session effectively clarified why inconsistent annotation and technical variability limit large-scale data reuse and AI-driven discovery, and they appreciated concrete examples involving SDRF, PRIDE/MassIVE, ML-based modeling, and deep-learning tools such as Prosit. The session was viewed as particularly valuable for trainees planning to work with large or legacy proteomics datasets.

Single-Cell Proteomics: Technologies and Applications:

7 respondents completed the survey for this session. Feedback indicated strong appreciation for the session’s clear evaluation of current single-cell proteomics technologies, including strengths, limitations, and appropriate use cases. Participants valued the balanced discussion of technical performance, data quality considerations, and biological interpretation, which helped them critically assess when and how single-cell proteomics approaches can be effectively applied. Several respondents noted that the session improved their ability to evaluate experimental design choices and technology readiness, rather than simply learning tool-specific workflows. Overall satisfaction was high, and respondents expressed interest in additional ETC offerings that similarly emphasize critical evaluation and practical decision-making in emerging proteomics technologies.

HUPO ECR Committee Webinar: Maximizing the Impact of your Abstract and Keywords

Mon, 02 Feb 2026 22:35:24 GMT

Register Now!

Join the HUPO Early Career Researcher Committee for an engaging webinar:

Maximizing the Impact of your Abstract and Keywords

March 4th | 16:00 GMT
Hear from international expert:
Reegan Burnell-Clarke – Taylor & Francis Commissioning Editor

Join Reegan Burnell-Clarke (Taylor & Francis Commissioning Editor) for a short session on "Maximising the impact of your abstract and keywords" to learn how these elements can make or break your research's discoverability and impact.

Discover how to craft a precise compelling title, write a concise and self-contained abstract, and strategically use effective keywords to maximize visibility and engagement. This session is well-suited for researchers striving to maximize the reach and influence of their scholarly contributions and will be followed by an opportunity for question and answers.

HUPOST January 2026

Fri, 30 Jan 2026 18:39:00 GMT

The HUPOST January 2026 issue is here!

Featuring: Congress Updates, ECR Highlights & Much More!

HUPOST January 2026: Congress Updates, ECR Highlights & Much More: https://conta.cc/49G7Clq

HUPO ECR Committee Welcomes New Members

Fri, 23 Jan 2026 22:23:56 GMT

The ECR Committee is pleased to welcome new members from all over the world. They will play key organizing roles in ECR activities such as mentoring sessions, networking events, online panel discussions, competitions, and more. Read their short biographies to get to know more about them.

Ankit Biswas is an Integrated MSc-PhD candidate at UNESCO-Regional Centre for Biotechnology, Department of Biotechnology, India. His research focuses on the conjunction between placental molecular markers in maternal plasma for early detection and maintenance of preterm birth. Further, elucidating the marker's mechanistic function in adverse pregnancy outcomes using advanced proteomic platforms. He is largely interested in exploring the field of reproductive biology employing new generation proteomic tools to bridge the knowledge gap between clinical outcome and molecular mechanism.

Moreover, as a member of proteomic society, India he has been a part of outreach programs for proteomics training in India. Ankit greatly looks forward to becoming a part of the HUPO-ECR community to actively contribute to the initiatives that support early-career researchers and foster dynamic interdisciplinary collaboration.

Beata Szeitz (Bea) is a postdoctoral fellow in the Fenyo Lab at NYU Langone Health. She earned her PhD from Semmelweis University in Hungary, focusing on lung cancer proteomics. Her research addresses biologically and clinically driven questions in cancer using bioinformatic approaches. In her postdoctoral work, she studies the role of LINE-1 retrotransposon in small cell lung cancer. Bea is glad to become a member of the HUPO-ECR and looks forward to contributing to its activities.

Mayara Silva (Maya) is a senior PhD candidate in Molecular and Cellular Biology at the University of Guelph, Canada. She completed her Bachelor’s degree in Pharmacy and her Master’s degree in fungal biology/medical mycology at the Universidade Federal de Pernambuco, Brazil. Throughout her academic journey, Mayara has been actively engaged in science communication initiatives, reflecting her commitment to connecting science with broader audiences.

Her research focuses on the application of mass spectrometry–based proteomics to investigate host–pathogen protein–protein interactions, with the aim of advancing our understanding of infectious disease development. By integrating clinical training with foundational biological research, she is particularly interested in translational science and in developing proteomics-based approaches to elucidate the interplay between immune responses and pathogen virulence factors.

Mayara is enthusiastic about joining the HUPO ECR Committee and looks forward to actively contributing to initiatives that support and empower early-career researchers within the global proteomics community.

Ragini Bhalla is a PhD candidate at Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), and is affiliated with the Department of Pharmacy and Pharmaceutical Sciences at the National University of Singapore (NUS). Her research examines how pancreatic ductal adenocarcinoma (PDAC) establishes an immunosuppressive tumour microenvironment that impairs CD8⁺ T-cell function. She leverages mass spectrometry-based proteomics, phosphoproteomics, and secretome profiling to study tumour-immune crosstalk and identify key dysfunctional pathways underlying impaired immune responses.

Her broader interests lie at the intersection of cancer biology and immunology, with a particular emphasis on applying high-resolution proteomics to uncover mechanisms of immune dysfunction and inform the rational design of next-generation immunotherapies.

Ragini looks forward to joining the HUPO-ECR community and actively contributing to initiatives that support early-career researchers and encourage interdisciplinary exchange.

Viviane Reber is a PhD student at the Institute of Molecular Systems Biology at ETH in Zurich, Switzerland. She works on developing and applying methods like limited proteolysis coupled to mass spectrometry (LiP-MS) and in vivo proximity labeling to understand the role of dynamic protein structures and how small molecules interact with protein targets. Her early work included a Master's thesis focused on Parkinson’s disease, specifically investigating how alpha-synuclein interacts with mitochondrial regulators of ATP homeostasis. Now she works on the characterization of chemical probes using multimodal proteomics with a focus on kinase inhibitors as part of the public-private partnership EUbOPEN.

Viviane joined the HUPO-ECR in October 2025 and is excited to continue to support and empower young researchers.

Call for the 2026 HUPO Early Career Researcher Manuscript Competition!

Fri, 23 Jan 2026 22:01:13 GMT

The HUPO Early Career Researcher (ECR) Committee is pleased to announce a call for the HUPO ECR Manuscript Competition, sponsored by Taylor and Francis, at HUPO 2026, which will take place September 27 - October 1, in Singapore. The Manuscript Competition is a unique opportunity for early career researchers to gain visibility in the proteomics community, as it serves as a platform to highlight the invaluable contributions that postdoctoral fellows, young clinicians, and junior faculty members make to the proteomics field.

We encourage early career proteomics researchers to participate in this competition with an already published or accepted manuscript during the 2025 and 2026 calendar years. Three finalists will be selected to present their publications in a dedicated plenary session at HUPO 2026, where an expert committee will evaluate oral presentations to determine the “Proteomics Highlight of the Year” by an ECR.

Eligibility criteria: This competition is intended for:

● Postdoctoral fellows (Ph.D. degree awarded post January 2020),

● Junior faculty members (appointment post January 2022 and PhD awarded post January 2014), and

● Young clinicians (M.D. degree awarded post January 2019).

● Applicants must be HUPO members.

● Career interruptions and leave, such as parental leave, will be considered to extend the eligibility period.

● Finalists from previous years are not eligible to participate.

Publication criteria:

● The applicant must have contributed significantly to the publication as the first or last (or shared first/last) author.

● The publication must be an original research article.

● Review articles will not be considered for this competition.

● The publication must have been accepted or printed for publication at the time of submission for the competition but must not have been published before January 1, 2025.

● Manuscripts that were posted on bioRxiv and other pre-print servers prior to publication will be considered (i.e., prior to January 1, 2025).

● The publication must be written in English.

How to Apply: A complete application must include the documents listed below. Send completed applications by email to ecr@hupo.org.

1. Single publication file as a pdf (including the supplementary information if it applies)

2. A short statement (300 words maximum) in which the applicant describes the novelty and impact of the publication on the field of proteomics.

3. Evidence of HUPO membership (e.g., screenshot of HUPO membership or member ID)

Prize: Awards will be presented during the Closing Ceremony & Awards Session at HUPO 2026. Cash prizes (USD 1,000 to winner and USD 500 each to two runners-up) will be provided post-Congress.

HUPOST December 2025

Fri, 19 Dec 2025 15:09:24 GMT

The HUPOST December 2025 issue is here!

Featuring: Congress Recap, ECR Winners Announced & Much More! https://conta.cc/4anEmkg

HUPO ECR Poster Competition

Mon, 15 Dec 2025 17:44:08 GMT

In a crowd hungry for knowledge, an intense poster competition has taken place. The contest has never been this close. Please welcome the winners of the ECR Poster Competition 2025! Our two champions and six runners-up should be proud of their outstanding presentations.

This year’s participants left the HUPO World Congress with honourable certificates and winners received prizes sponsored by Pelago Bioscience. Congratulations to all, and we look forward to seeing new rising stars at HUPO 2026 in Singapore!

Students:

Winner

Daniel Davoudpour, Masters Student

University Of Toronto, Canada

Affinity-purification mass spectrometry (AP-MS) and kinase inhibitor screens identify phosphorylation-mediated regulation of αT-catenin at the cardiomyocyte intercalated disc.

Runner-up

Marion Pang, PhD student

California Institute of Technology, United States

Marker-guided Spatial Proteomics by LMD-ScP Captures Single-Cell Identity and Heterogeneity of the Nervous System

Runner-up

Kathrin Korff, PhD student

Max Planck Institute of Biochemistry, Germany

Sample handling shapes the signal: workflow bias in plasma proteomics.

Runner-up

Martin Gesell, PhD student

ETH Zurich, Switzerland

Specialized T Cell Receptor Nanoscale Communities Define Subset Diversity of Primary Human T Cell Subsets.

Post-Docs:

Winner

Marc Oeller, Postdoctoral Fellow

Max Planck Institute of Biochemistry, Germany

Resolving the Heterogeneity of Protein Inclusions in Parkinson’s Disease by Deep Visual Proteomics

Runner-up

Ana Montero, Postdoctoral Fellow

Instituto De Salud Carlos Iii, Spain

In depth-analysis of Alzheimer’s disease brain tissue reveals novel Aβ interactors

Runner-up

Loren Méar,Postdoctoral Fellow

Uppsala University, Sweden

Spatial proteomics uncovers structural and molecular complexity of the human ovary in 2D and 3D.

Runner-up

Ulises H. Guzman, Postdoctoral Fellow

NNF Centre For Protein Research, ICMM, UCPH, Denmark

A Scalable FFPE tissue Workflow for High-Throughput and Sensitive Spatial Proteomics

HUPO ECR Poster Competition prizes sponsored by Pelago Bioscience.

Congratulations to the winner of the 3-Minute Thesis (3MT) Competition, Ruxandra Bighiu!

Mon, 15 Dec 2025 16:30:46 GMT

The 3MT Competition at HUPO was a truly inspiring showcase of creativity, clarity, and scientific communication. Twelve PhD students embraced the challenge of presenting their complex research in just three minutes, using only one static slide and speaking as if to a lay audience. Their ability to distil intricate proteomics topics into accessible, engaging presentations was remarkable, demonstrating impressive precision, confidence, and dedication. The session captivated everyone in the room and highlighted the strength of the next generation of researchers. A standout moment came from Ruxandra Bighiu, who captivated the audience with the fascinating world of hearing proteins.”

Winner

Ruxandra Bighiu, University Of Antwerp, Antwerp, Belgium

The Hidden Machinery of Hearing: A Deep Dive into Hearing Proteins

Runner-up

Caroline Weiss, Max Planck Institute of Biochemistry, München, Germany

Mapping the Protein Landscape of the Human Body

Runner-up

Carla-Marie Jurkovic, Université De Sherbrooke, Sherbrooke, Canada

Uncovering the hidden mechanics of DNA repair to fight cancer

All prizes are sponsored by Mass Dynamics and will be awarded post-congress: $500 for the Winner and $300 each for two Runners-up, plus an annual subscription to Mass Dynamics software for the Winner and both Runners-up.

Congratulations to the winner of the HUPO 2025 ECR Manuscript Competition, Dr. Xiang Zheng!

Mon, 15 Dec 2025 16:08:37 GMT

The Early Career Researcher Manuscript Competition was a fierce competition!

Our three finalists, Dr. Xiang Zheng (Aarhus University), Dr. Arun Vadivel (SickKids Hospital), and Dr. Julia Bubis (Vienna BioCenter) each gave fantastic talks at the dedicated oral session sponsored by Taylor & Francis. Deciding a winner was no easy feat for our panel of expert judges. In the end, Dr. Xiang Zheng was awarded the first-place winning title of Proteomics Highlight of the Year and a cash prize of $1000. Congratulations to Dr. Zheng and the two runners-up, Dr. Vadivel and Dr. Bubis (cash prize of $500 each)!. Dr. René Zahedi (Taylor & Francis, University of Manitoba) and Roshan Tosh Aggarwal (HUPO ECR Committee member, University of Guelph) chaired the competition.

Winner

Dr. Xiang Zheng, Assistant Professor

Aarhus University, Denmark

Deciphering Functional Tumor-Immune Crosstalk Through Highlight Multiplexed Imaging and Deep Visual Proteomics

Runner-up

Dr. Arun Vadivel, Research Fellow

SickKids Hospital, Canada

The Proteomic Landscape of Diffuse Midline Glioma Highlights the Therapeutic Potential of Non-Histone Protein Methyltransferases

Runner-up

Dr. Julia Bubis, Post-doctoral Researcher

Vienna BioCenter, Vienna

Challenging the Astral Mass Analyzer to Quantify up to 5,300 Proteins Per Single Cell at Unseen Accuracy to Uncover Cellular Heterogeneity

We would like to extend a huge thank you to our competition sponsor, Taylor and Francis, for helping to make this competition possible!

Announcing the HUPO Award 2025 Winners!

Thu, 30 Oct 2025 11:41:24 GMT

We are delighted to announce the recipients of the HUPO Awards 2025, celebrating outstanding contributions to the global proteomics community.

View the full list of HUPO Awards 2025 recipients.

The winners will be formally recognized during the HUPO 2025 Congress — we encourage all attendees to join us in celebrating their achievements and cheering them on!

HUPOST October 2025

Wed, 22 Oct 2025 21:16:35 GMT

The HUPOST October 2025 issue is here!

Featuring: Congress Updates, Election Reminder, Updates from ECR Committee & Much More https://conta.cc/3W7ZjqT

HUPOST September 2025

Mon, 15 Sep 2025 18:58:10 GMT

The HUPOST September 2025 issue is here!

Featuring: Congress Updates and Deadlines, Election News, Updates from ECR Committee, ETC Webinar & Much More https://conta.cc/4n3mfU4

Get Ready for the 3-Minute Thesis (3MT) Competition Final!

Mon, 08 Sep 2025 20:37:36 GMT

The moment you've been waiting for is almost here! We're thrilled to announce the incredible finalists for this year's 3-Minute Thesis (3MT) Competition. After a fierce selection process, these exceptional researchers are ready to take the stage and share their groundbreaking work.

In a high-stakes, high-energy event, each finalist will have just three minutes to present their research, using only a single static slide. Get ready to be amazed as they distill complex ideas into captivating, easy-to-understand presentations.

Don't miss the final on Monday, November 10th, from 4:30 to 5:35 PM. Come see who will be crowned this year's champion by our expert judging panel and a live audience!

Meet HUPO 2025 ECR Manuscript Competition Finalist: Dr. Xiang Zheng!

Mon, 08 Sep 2025 20:07:15 GMT

We hope you’re as excited as we are for this year’s HUPO Early Career Researcher Manuscript Competition! You absolutely won’t want to miss our finalists presenting their work: Dr. Arun Vadivel (SickKids, Canada), Dr. Julia Bubis (Vienna BioCentra, Austria), and Dr. Xiang Zheng (Aarhus University, Denmark). Join us for their dedicated session at HUPO 2025 in Toronto, Canada, on Tuesday November 11th at 9:10am, where the winner of this year’s competition will receive a cash prize of USD$1000 and both runners-up will each receive USD$500. This is a session you won’t want to miss!

Last, but certainly not least, we would like you to meet Dr. Xiang Zheng, an assistant professor at Aarhus University:

After earning a Bachelor of Clinical Medicine, he embarked on cancer research during his master's studies at Peking University, China. He later pursued a PhD in Human Biomedicine at the Max Planck Institute, Germany, specializing in multiplexed staining-based lung cancer biomarker identification and tumor microenvironment reprogramming.

In 2021, Dr. Zheng joined the group of Prof. Matthias Mann at the University of Copenhagen as a postdoctoral researcher, where he integrated multiplexed immunofluorescence imaging with Deep Visual Proteomics (mipDVP) to advance spatial proteomics and resolve tumor–immune interactions at single-cell resolution. Since 2024, he has been an Assistant Professor in Spatial Proteomics at Aarhus University under the support of Prof. Robert A. Fenton, focusing on applying mipDVP to drive precision medicine research in cancer, kidney diseases, and neurodegenerative disorders.

He has authored 18 peer-reviewed publications—including 10 as first author and 3 as corresponding author—in journals including Molecular Cell, Nature Communications, and Cancer Research. His work has been recognized with 12 awards, including the Emerging Technologies Funding Award, the Danish Bioimaging Image Contest Prize, and the William MacNee Award.

We would like to extend a huge thank you to our competition sponsor, Taylor and Francis, for helping to make this competition possible!

Call for Nominations: HUPO EC - VICE PRESIDENT

Wed, 03 Sep 2025 21:01:37 GMT

Nominations are now open for a HUPO Executive Committee position of Vice President. This is an opportunity to lead and shape the future of a significant scientific organization and work with an enthusiastic global team to promote and represent proteomics.

The Executive Committee (EC) of the Human Proteome Organization consists of fourteen officers as follows: President, Immediate Past President or President-Elect, Vice President, Secretary General, Treasurer, two Members-at-Large, ECR representative, two HPP, two C/HPP and two B/D HPP representatives

All positions are elected by the vote of HUPO Council.

Executive Committee nominees must be active (paid) HUPO members and scientists from the public or private sector with professional experience in the educational, research, or commercial activities related to the purposes of HUPO.

The following Executive Committee position will be elected by Council vote for commencing in January 2026:

· Vice President (2026-2027)

Click here to view a list of the current HUPO Executive Committee.

To submit a self-nomination, complete the Nomination Form here and include a headshot photo.

Deadline to submit self-nominations - September 16 - 11:59 pm PDT.

For questions or further information, please contact the HUPO Office office@hupo.org

HUPOST August 2025

Fri, 22 Aug 2025 20:42:23 GMT

The HUPOST August 2025 issue is here!

Featuring: 2025 Congress Updates, News from ECR Committee, & Much More! https://conta.cc/4oN9xKA

Meet the finalist of the HUPO 2025 ECR Manuscript Competition: Dr. Julia Bubis!

Thu, 14 Aug 2025 05:57:00 GMT

Welcome back, as we continue to introduce the finalists of this year’s HUPO Early Career Researcher Manuscript Competition: Dr. Arun Vadivel (SickKids, Canada), Dr. Julia Bubis (Vienna BioCentra, Austria), and Dr. Xiang Zheng (Aarhus University, Denmark)! They will be presenting their work in a dedicated session at HUPO 2025 in Toronto, Canada, on Tuesday November 11th at 9:10am. The winner of this year’s ECR Manuscript Competition will receive a cash prize of USD$1000 and both runner-ups will each receive USD$500. This is a session you will not want to miss!

This month, we would like you to meet Dr. Julia Bubis, a postdoctoral fellow at the Vienna BioCenter:

Julia Bubis, PhD, is a molecular and chemical physicist specializing in high-throughput LC-MS method development and quantitative proteomics. She earned her PhD from the Moscow Institute of Physics and Technology, where she focused on innovative analytical strategies for cellular proteome profiling. As a postdoctoral fellow at the Vienna BioCenter, Julia leads the "Single-cell Proteomics of Human Blastoid" project, which is supported by the Austrian Academy of Sciences. This project focusses on developing LC-MS techniques for single-cell proteomics and data analysis to better understand the mechanisms of early-stage embryo development using blastocyst-like structures.

Another big thank you as well to our competition sponsor, Taylor and Francis!

4th annual Ubuntu Proteomics Summer School (UPSS)

Thu, 14 Aug 2025 05:21:10 GMT

“Sunshine and Happiness”

Registrations are now open for the 4^th annual Ubuntu Proteomics Summer School (UPSS). If you are in the northern hemisphere currently enjoying some sunshine, fast forward ±6 months from now and plan to attend the school where you can get a fresh dose of Vitamin D!

And the icing on the cake is the amazing list of speakers and wonderful course content. The next event will be held in George, along the Garden Route in South Africa, February 1-7, 2026. See last year’s event in Ballito, view the video linked here.

Join us and listen to talks from the likes of Jesper Olsen, Bernhard Küster, Kathryn Lilley and more.

View the complete list of speakers here.

The Ubuntu Proteomics Summer School (UPSS) is a one-week residential school with a concepts and applications track. The summer school aims to help researchers:

Learn more about proteomics from leading experts in the field
Connect to new networks and create collaborative opportunities
Explore new and dynamic locations (the summer school is a “floating” one and consequently changes location each year)
Grow capacity to advance proteomics-driven research in multiple fields

Feel free to explore galleries from our 2023 and 2024 schools or watch some videos on our YouTube channel, or explore our X, Bluesky and LinkedIn profiles.

If you are interested in attending then please apply here or spread the word to any interested parties.

#ubuntuproteomics

OBO the UPSS Organising Committee

Call for Nominations: HUPO Council

Wed, 23 Jul 2025 15:10:26 GMT

HUPO is seeking candidates to serve on the HUPO Council for a three-year term beginning January 2026 (2026 - 2028).

Each Councilor must be an active (paid) HUPO member who is a scientist from the public or private sector with professional experience in educational, research, or commercial activities related to the purposes of HUPO. HUPO Councilors are expected to actively participate in at least one HUPO Committee, Initiative or Working Group and assist with other HUPO activities from time to time, during their term.

By serving in a leadership capacity, you can further the priorities outlined in the HUPO strategic plan and enhance your professional profile and organization among peers and across the proteomics community. HUPO embraces diversity and inclusion and is committed to building an organization that represents a variety of identities, backgrounds, perspectives and abilities. In 2017 HUPO Council removed the clause that requires Councilors to have at least ten years of professional experience.

We invite you to submit a nomination or self-nomination.
Click here to open the nomination form
The deadline for all nominations is July 31, 2025.

For questions or further information, please contact the HUPO Office office@hupo.org

HUPOST July 2025

Wed, 16 Jul 2025 15:05:41 GMT

The HUPOST July 2025 issue is here!

Featuring: HUPO Council - Call for Nominations, 2025 Congress Updates, News from ECR Committee, ETC Webinars, & Much More! https://conta.cc/4nWJz6U

HUPO ECR Committee Welcomes a New Member

Wed, 09 Jul 2025 21:21:49 GMT

Jianbo Fu

Jianbo is a postdoctoral researcher at the Swiss Multi-Omics Center (SMOC) and ETH Zürich. His work focuses on computational frameworks for complex disease identification and therapeutic target discovery using multi-omics data. He has developed online platforms for large-scale omics data processing, improving accuracy and reproducibility. He also built a cross-cohort database of plasma metabolite–cytokine networks and designed multimodal pathway analysis strategies to reveal key mechanisms in complex diseases. He has published 24 peer-reviewed papers, including 10 as first/co-first author in Nature Protocols, with over 1,300 citations. His future work will focus on advancing multimodal omics integration to precisely identify disease-driving targets and developing innovative computational tools for complex disease research and drug discovery.

Meet HUPO 2025 ECR Manuscript Competition finalist: Dr. Arun Vadivel!

Wed, 09 Jul 2025 21:10:28 GMT

This month, we’d like you to meet Dr. Arun Vadivel:

Dr. Arun K Anguraj Vadivel, PhD is a postdoctoral research fellow in the Brain Tumour Research Centre at SickKids, Toronto. His work integrates multi-omics using machine learning (ML), and experimentation to advance precision medicine for paediatric brain tumours, especially diffuse midline glioma (DMG). Leveraging whole-genome/exome sequencing, RNA-seq, DNA-methylation arrays, quantitative proteomics, post translational modifications, and metabolomics, he built pipelines that fuse these layers with similarity network fusion, NetDx, and in-house pipeline using scikit-learn. His integrative approach pinpointed METTL13 as a therapeutic dependency in DMG; inhibition extends survival in xenograft models and was published in Neuro-Oncology (2025). In parallel, he showed that dietary methionine restriction prolongs survival in DMG models and created a protein-based ML classifier that distinguishes six paediatric brain tumour entities with 99 % accuracy.

Dr. Anguraj Vadivel’s vast bench-to-bioinformatics experience spans protein purification, LC–MS/MS, DDA/DIA MS data analysis, and NGS workflows. He has discovered cerebrospinal-fluid biomarkers that may enable minimally invasive patient monitoring. Former experience as Biomedical Data Analyst at BenchSci and PhD at Western University sharpened his ability to translate datasets into actionable insights for both academic and industry stakeholders. A committed leader, he collaborates with teams across SickKids, Carleton University, and the University of Toronto, and has mentored seven trainees on projects ranging from synthetic-peptide therapeutics to liquid biopsy. His grant-writing contributions have secured over CAD 500,000 in external funding and underpin a CAD 1.8 million CIHR proposal now under review. He belongs to the Society for Neuro-Oncology and the Human Proteome Organization, serves as a reviewer for Scientific Reports and Brain Pathology, and has delivered lectures and award-winning presentations on three continents. These accomplishments and his expertise in proteomics, data integration, and bioinformatics position Dr. Anguraj Vadivel to excel as a rising scientist dedicated to enhancing protein-based diagnostics and improving patient outcomes.

Another big thank you as well to our competition sponsor, Taylor and Francis!

HUPOST June 2025

Wed, 11 Jun 2025 15:53:32 GMT

The HUPOST June 2025 issue is here!

Featuring: 2025 Congress Updates, News from ECR Committee, ETC Webinar, B/D HPP Presentations & Much More! https://conta.cc/3FT52w8

HUPOST May 2025

Fri, 16 May 2025 17:07:14 GMT

The HUPOST May 2025 issue is here!

Featuring: 2025 Congress Updates, HUPO Award Nominations Deadline, News from ECR Committee, ETC Webinar & Much More! https://conta.cc/3YLg3pE

Applications are open for the HUPO Rising Star Award!

Mon, 12 May 2025 16:23:52 GMT

Are you or do you know an ECR who deserves to be recognized for their contribution to the proteomics community? The HUPO Rising Star Award recognizes early career researchers who have had an exceptional impact on the proteomics field, whether that be through publications, patents, commercialization, education or any other contribution or service to the field of proteomics.

We caught up with last year’s HUPO Rising Star, Lindsay Pino, to ask why should an ECR apply for this award:

“Having a non-traditional, winding path through training and career trajectory, I wasn’t sure if my contributions really fit the right profile for the Rising Star award. It turns out that’s exactly the point! This award recognizes the many ways the community contributes to proteomics as a field, not only the conventional ones. So if you’re doing something a little off the typical path in proteomics, make sure to shoot your shot and apply. This award has really shown me that the field is stronger because of the many different ways proteomicists show up in the world.”

Candidates can self-nominate or be nominated (by a supervisor, colleague, superior, client, collaborator, etc). Our first-place winner will receive a cash prize of USD $2000. The award will be presented at HUPO 2025 in Toronto, Canada alongside the opportunity to provide a short talk.

The deadline to apply is May 16, 2025.

To learn more about eligibility criteria and how to apply, click here.

Join ECR Mentoring Sessions at the HUPO World Congress 2025

Mon, 12 May 2025 16:10:29 GMT

The Early Career Researcher (ECR) Committee is excited to present this year’s Mentoring Sessions—an open and supportive space where mentors and mentees can connect and explore key topics around building a successful early career. Three engaging sessions will be held during the HUPO World Congress in Toronto, Canada. Don’t miss the chance to attend, get involved in the conversation, and ask your questions!

What are we going to discuss:

● From PhD to Profession: Navigating Diverse Career Opportunities

Scientific skills can be applied to many professions. Explore your opportunities to make a mindful decision about your next career step.

● Maximizing Your Research Impact: A Strategic Publication Plan

Unlike fiction writing, scientific communication must be tailored to the specific audience of the target journal. In this session, we’ll share practical strategies and insights on how to avoid long publication delays and ensure your research reaches the right audience efficiently.

● Interdisciplinary Science: Communicating and Collaborating Across Fields

Proteomics sits at the crossroads of physics, chemistry, biology, medicine, engineering, and computer science. Unraveling the mysteries of protein function demands genuine interdisciplinary collaboration. Together, we will explore how effective communication can help you thrive in a diverse, cross-functional team.

The ETC Committee welcomes its newest member, Dr. Sayantani Chatterjee

Fri, 09 May 2025 20:30:20 GMT

Sayantani Chatterjee, PhD (Australia) is currently a posdoctoral research fellow in the Analytical Glycoimmunology Group from Macquarie University in Sydney.

Her research encompasses cancer glycoimmunology. Previously, she was a postdoctoral associate at Boston University and her research focused on investigating viral glycoproteomics, particularly of Influenza and SARS-CoV-2, using ion mobility mass spectrometry. She is originally from India where she received her BSc in Microbiology (Honours) (2015) from St. Xavier’s College (Autonomous) and moved to Australia to pursue Master of Research (2017) and subsequently PhD (2021) in the Analytical Glycoimmunology Group focusing on mannose-terminating glycoproteins involved in human health and disease.

She has been a HUPO ECR member since 2022 and was also the Vice-Chair Logistics (2-year term) for the 22^nd and 23^rd HUPO World Congresses.

BD-HPP Presentation Q2 - SCI & Metaproteomics

Wed, 23 Apr 2025 15:04:31 GMT

Date: June 9, 2025

Time: 10:00am EST

Presenters:

Claudia Ctortecka - SCI Initiative
Benoit Kunath - Metaproteomics Initiative
Susana Cristobal - iMOP

HUPO ETC Webinar Series: Pathology, Proteomics and Precision Medicine - Prof. Ed. Nice

Wed, 09 Apr 2025 15:46:44 GMT

The HUPO Education and Training Committee is excited to announce a webinar series focused on the critical role of proteomics in Clinical investigation. This series will have 6 webinars at ~1 month intervals and bring together leading experts to discuss the latest advancements, challenges, and opportunities in applying proteomics to improve human health. This webinar series is designed for researchers, clinicians, and anyone interested in learning more about the exciting field of clinical proteomics.

Title: Pathology, Proteomics and Precision Medicine

Speaker: Prof. Ed. Nice

Date: Thursday 24^th April 2025

Time: 10:00 UTC

Registration: https://us06web.zoom.us/webinar/register/WN_8_8Xm0rlRRSZvV36Exgw7g

Previous webinars:
You can find a playlist with videos for Series 1 and 2 of the HUPO ETC Webinar focused on Scientific Writing and Focus on Technology here: https://bit.ly/etc_webinars

HUPOST April 2025

Wed, 09 Apr 2025 14:49:24 GMT

The HUPOST April 2025 issue is here!

Featuring: 2025 Congress Updates, HUPO Award Nominations Now Open, News from the ECR Committee ETC Webinar & Much More! https://conta.cc/4jsLzRb

The 2025 HUPO ECR Poster Competition is still open for entries!

Wed, 02 Apr 2025 16:39:56 GMT

SUBMISSION DEADLINE: May 16, 2025

The HUPO Early Career Researcher (ECR) initiative invites all graduate students and postdocs to participate in the Poster Competition at HUPO 2025 happening November 9 - 13 in Toronto, Canada. Showcase your work to win awards and cash prizes!

Eligibility Criteria: All graduate students (Master's and PhD) and postdocs can apply for the competition upon abstract submission for HUPO 2025. Applicants must be HUPO members.

How to Apply: During the abstract submission procedure for HUPO 2025, Master’s students, PhD students, and postdocs must indicate if they want to also participate in the poster competition.

Selection Criteria: 15 posters in each category (graduate students and postdocs) will be pre-selected based on quality, novelty, and potential impact of their abstracts. Presenters of selected posters will be notified before the conference.

On-site Evaluation: Posters will be visited by evaluators during the poster sessions at HUPO 2025.

Prize: $500 will be awarded to the winner and $300 to the runner-up in both the graduate student and postdoc competitions.

Visibility: Award winners will be highlighted during the HUPO 2025 Closing Ceremony & Awards Session

There’s still time! We’ve extended the deadline for the HUPO Early Career Researcher Manuscript Competition to May 4th, 2025

Wed, 02 Apr 2025 16:25:37 GMT

You haven’t missed your chance to submit to the HUPO Early Career Researcher Manuscript Competition! Submit your original research article, from the past year, by May 4th, 2025, for a chance to present your work at HUPO 2025 in Toronto, Canada. This competition, sponsored by Taylor and Francis, is a unique opportunity for early career researchers to gain visibility within the broader proteomics community.

We encourage early career researchers - postdoctoral fellows, young clinicians, and junior faculty - with a publication or accepted manuscript in the 2024 and 2025 calendar years to participate. Three finalists will be selected to present their work in a dedicated plenary session at HUPO 2025, where an expert committee will determine the “Proteomics Highlight of the Year” by an early career researcher.

Eligibility criteria: This competition is intended for postdoctoral fellows (Ph.D. degree awarded post January 2019), junior faculty members (appointment post January 2021 and PhD awarded post January 2013), and young clinicians (M.D. degree awarded post January 2018). Applicants must be HUPO members. Career interruptions and leaves, such as parental leaves, will be considered to extend the eligibility period. Finalists from previous years are ineligible to participate.

Publication criteria: The applicant must have significantly contributed to the publication as a first or last (or shared first/last) author. The publication must be an original research article. Review articles will not be considered for this competition. The publication must have been accepted or printed for publication at the time of submission for the competition but must not have been published before January 1, 2024. Manuscripts that were posted on bioRxiv and other preprint servers prior to submission will be considered.

How to Apply: A complete application needs to include the documents listed below. Send completed applications by email to ecr@hupo.org.

Single publication file as a pdf (including the supplementary information, if it applies):

○ The manuscript must be an original research article and the applicant must have contributed significantly to the concept and/or experimental work and/or data analysis (first, co-first, corresponding or co-corresponding author).

○ The publication must have been accepted and/or printed for publication at the time of submission to the competition, but not earlier than January 1, 2024.

○ The publication must be in English.

2. A short statement (300 words maximum) in which the applicant describes the novelty and impact of the publication on the field of proteomics.

Deadline to apply: May 4, 2025

We’re looking for the next HUPO Rising Star!

Wed, 02 Apr 2025 16:17:33 GMT

The HUPO Early Career Researcher (ECR) initiative is proud to present an award to recognize rising stars and leaders in the field of proteomics. This career achievement award is designed to recognize early career researchers who have had an exceptional impact on the proteomics field and community. This impact can take the shape of publications, patents obtained, development of a commercial product, establishment of a course, training program, workshop or any other contributions or service to the field of proteomics. The winner of the award will give a short presentation during the closing ceremony of HUPO 2025 and take home a cash prize of USD $2000.

Nominations are open to all HUPO members who have accumulated at most 5 years after their Ph.D. defense, by the application deadline. Ph.D. Career interruptions and leaves, such as parental leaves, will be taken into account to extend the eligibility period. Candidates can self-nominate or be nominated, by a supervisor, a colleague, a superior, a client, a collaborator, etc. The person nominating the candidate can be anybody that has been positively impacted or has witnessed the positive impact of the nominee.

Eligibility criteria: Open to HUPO members who have accumulated at most 5 years after their Ph.D. defense, by the application deadline. Ph.D. Career interruptions and leaves, such as parental leaves, will be taken into account to extend the eligibility period.

Nomination Process: Candidates can self-nominate or be nominated, by a supervisor, a colleague, a superior, a client, a collaborator, etc. The person nominating the candidate can be anybody that has been positively impacted or has witnessed the positive impact of the nominee.

Application Package: Short description of nominee’s career stage, most significant contributions, how the contributions impact the field of proteomics, the breadth of the contributions and their originality.

Selection Criteria: Award is given based on the overall career achievements of the nominee, whether those are publications, patents obtained, development of a commercial product, establishment of a course, training program, or workshop. 60% of the score is based on the impact of the nominee on the field or community and the other 40% on the originality and breadth of the contributions to the field or community.

Prize: Cash Prize of USD $2000. The award will be given at HUPO 2025 and accompanied by a short talk. The winner will be asked to provide a short biosketch and a headshot photograph for publication and advertising purposes.

Click here to submit your application. Deadline Friday 16th May

31st C-HPP Symposium

Wed, 02 Apr 2025 14:51:37 GMT

On behalf of C-HPP EC, we invite you to attend the upcoming 31st C-HPP Symposium "Navigating the Uncharted Waters of Protein Function" which will be held on June 12-14 in Saint-Malo, France. The symposium will provide an opportunity to discuss the latest developments in the Chromosome-Centric Human Proteome Project (C-HPP) towards the Grand Challenge and explore future research directions.

The C-HPP Symposium will take place June 16-20, just before the EuPA 2025 Conference

This is an excellent opportunity to also attend EuPA2025 and engage with a broader scientific community. Enjoy the stunning surroundings and serene atmosphere of Saint-Malo as you connect and engage informally with the Proteomics community for meaningful exchanges.

Please note that registration to the C-HPP Symposium is independent from that of EuPA2025.

Should you plan to attend the symposium, please register here by April 14.

Looking forward to welcoming you in the Corsair city.

Easy route to Saint-Malo:

From Paris CDG airport.

· Take TGV Train to Rennes at Terminal 2D (2h45 min). Once in Rennes, take the TER shuttle to Saint-malo (50 min)

From Paris City center. At Gare Montparnasse, two options :

· Train to Rennes (1h25 min) + TER shuttle to Saint Malo (50 min) (20 trains/Day)

· Direct Train to Saint-Malo (2h15 min) (5 trains/Day)

31th C-HPP workshop

Navigating the Uncharted Waters of Protein Function

Hôtel France et Chateaubriand Saint-Malo

June 12-14, 2025; Saint Malo, France

Thursday, June 12:

14:00-14:10	Welcome (Gong Zhang, Charles Pineau)
14:10-15:40	Discussion on Guidelines for Assigning Protein Function for the Grand Challenge (Charles Pineau, Gong Zhang, Eric Deutsch)
15:40-16:00	Coffee Break
16:00-16:30	AI-based Protein Structure Using HelixFold3 (Yueyang Huang)
16:30-18:00	Discussion on Guidelines for SWATH/DIA Data into HPP (Eric Deutsch)
Metrics of the Human Proteome Project (Eric Deutsch)
19:00-	Welcome Dinner (TBA)

Friday, June 13:

09:30-10:20	C-HPP Overview and Activities (Gong Zhang, Chris Overall)
10:20-10:45	HPP Portal Updates (Gong Zhang)
10:45-11:10	Keynote Talk 1 TBA (Joshua LaBaer)
11:10-11:35	Keynote Talk 2 TBA (TBA)
11:35-12:00	Systematic in vitro Translation of the Dark Human Proteome (Yao Wang)
12:00-13:30	Plaque Ceremony, Photo Time and Lunch (for Joshua, Carapito, Louise)
13:30-13:45	C-HPP Team Report of Chr. 17 (Ed Nice)
13:45-14:00	Finding missing protein of Chr. 11 from sarcoma tissue (Heeyoun Hwang)
14:00-14:15	Integrating the Chr2 into the Danish proteomics community. (Allan Stensballe)
14:15-14:30	What we do for personal health monitoring: Chromosome 18 and more (Oxana Trifonova)
14:30-14:45	C-HPP Team Report (Michaela Cichinelli)
14:45-15:00	Coffee Break
15:00-15:25	Investigating Small Open Reading Frame - Encoded Peptides with Proteomics and Bioinformatics Techniques (Cuihong Wan)
15:25-15:50	Study of BALF to Discover Biomarkers for Lung Cancer (Min-Sik Kim)
15:50-16:15	Keynote Talk 6 TBA (Fernando Corrales)
16:15-16:40	Functional Annotation of Missing Proteins Using Bioactive Small Molecules (Ho Jeong Kwon)
16:40-18:00	Free Discussion
19:00-	Dinner (TBA)

Saturday, June 14:

09:30-10:30	In-depth Spatial Profiling of the Human Proteome, a First Step Towards Understanding Protein Function (Cecilia Lindskog)
10:30-11:00	Proteolytic Proteoforms in Viral Infection (Chris Overall)
11:00-11:30	Identifying New Protein Variants Through Proteogenomic Data Integration (Peter Horvatovich)
11:30-12:00	Discovering Clues to Protein Function in Public Databases: Can We Make It Easier? (Marie Locard-Paulet)
12:00-13:30	Lunch
13:30-14:00	Keynote Talk TBA (Viviana Greco)
14:00-14:30	Keynote Talk TBA (TBA)
14:30-15:00	Conclusion and Warp up

Supported by:

HUPOST March 2025

Mon, 17 Mar 2025 16:00:40 GMT

The HUPOST March 2025 issue is here!

Featuring: 2025 Congress Updates, ETC Webinars, News from the ECR Committee & Much More! https://conta.cc/4i2GaQx

Keep an eye out for the HUPO Rising Star Award

Wed, 05 Mar 2025 21:10:37 GMT

Prize: Cash Prize of USD $500. The award will be given at HUPO 2025 and accompanied by a short talk. The winner will be asked to provide a short biosketch and a headshot photograph for publication and advertising purposes.

Applications open soon.

The 2025 HUPO ECR Poster Competition is open for entries!

Wed, 05 Mar 2025 20:47:47 GMT

SUBMISSION DEADLINE: May 16, 2025

Eligibility criteria: All graduate students (Master's and PhD) and postdocs can apply for the competition upon abstract submission for HUPO 2025. Applicants must be HUPO members.

How to Apply: During the abstract submission procedure for HUPO 2025, Master’s students, PhD students, and postdocs must indicate if they want to also participate in the poster competition.

Selection criteria: 15 posters in each category (graduate students and postdocs) will be pre-selected based on quality, novelty, and potential impact of their abstracts. Presenters of selected posters will be notified before the conference.

On-site evaluation: Posters will be visited by evaluators during the poster sessions at HUPO 2025.

Prize: $500 will be awarded to the winner and $300 to the runner-up in both the graduate student and postdoc competitions.

Visibility: The award winners will be highlighted during the HUPO 2025 Closing Ceremony & Awards Session.

Don’t miss your chance to apply for the 2025 HUPO Early Career Researcher Manuscript Competition!

Wed, 05 Mar 2025 20:07:48 GMT

Have you published an original research article in the last year? Submit your work to the HUPO Early Career Researcher Manuscript Competition, sponsored by Taylor and Francis, for a chance to present your work at HUPO 2025 in Toronto, Canada! This competition is a unique opportunity for early career researchers to gain visibility within the broader proteomics community.

We encourage early career researchers - postdoctoral fellows, young clinicians, and junior faculty - with a publication or accepted manuscript in the 2024 and 2025 calendar years to participate. Three finalists will be selected to present their work in a dedicated plenary session at HUPO 2025, where an expert committee will determine the 'Proteomics Highlight of the Year' by an early career researcher.

Eligibility criteria: This competition is intended for postdoctoral fellows (Ph.D. degree awarded post January 2019), junior faculty members (appointment post January 2021 and PhD awarded post January 2013), and young clinicians (M.D. degree awarded post January 2018). Applicants must be HUPO members. Career interruptions and leaves, such as parental leave, will be considered to extend the eligibility period. Finalists from previous years are not eligible to participate.

Publication criteria: The applicant must have contributed significantly to the publication as the first or last (or shared first/last) author. The publication must be an original research article. Review articles will not be considered for this competition. The publication must have been accepted or printed for publication at the time of submission for the competition but must not have been published before January 1, 2024. Manuscripts that were posted on bioRxiv and other preprint servers prior to submission will be considered.

How to Apply: A complete application must include the documents listed below. Send completed applications by email to ecr@hupo.org.

Single publication file as a pdf (including the supplementary information, if it applies):
- The manuscript must be an original research article and the applicant must have contributed significantly to the concept and/or experimental work and/or data analysis (first, co-first, corresponding or co-corresponding author).

The publication must have been accepted and/or printed for publication at the time of submission to the competition, but not before January 1, 2024.

The publication must be in English.

2. A short statement (300 words maximum) in which the applicant describes the novelty and impact of the publication on the field of proteomics.

Deadline to apply: March 28, 2025

6th InPPO Conference

Wed, 05 Mar 2025 19:22:19 GMT

EARLY REGISTRATIONS EXTENDED TO MARCH 7
LATE BREAKING ABSTRACT SUBMISSIONS ACCEPTED UNTIL MARCH 7

The scientific program features keynote and invited speakers from around the world covering innovation within proteomics themes of single-cell/cell-type, interactions and modifications, technological advances, climatic resiliency, crops and agriculture, unconventional plants, and artificial intelligence in plant discovery.

Find registration details here and an overview of the program here!

HUPOST February 2025

Thu, 13 Feb 2025 13:59:11 GMT

The HUPOST February 2025 issue is here! Featuring:

2025 Congress Updates,

Call for the 2025 HUPO Early Career Researcher Manuscript Competition Submissions,

New Webinar News from the Education Committee

& Much More! https://conta.cc/4aFRkIf

30th Chromosome-Centric Human Proteome Project Workshop

Wed, 29 Jan 2025 19:00:48 GMT

The 30th C-HPP Workshop was held on November 29 in Guangzhou, China. 11 speakers from 5 countries presented their most recent work in the program that was topical and provocative. The meeting was well attended with 353 attendees (male:female ratio was 2:3 and the speakers 7:4) ensuring long and deep questions and discussion after all talks. In the workshop, we discussed novel proteoforms from sORF-encoded peptides, lncRNA-encoded dark proteome, and new splice isoforms, AI approaches in proteomics, and proteomic application in clinical treatment. Three talks were on the AI focus of the meeting, including the artificial neural network for glycopeptide classification, using generative AI to provide dynamical models on spatiotemporal single-cell omics data, and real-time peptide identification using end-to-end deep learning method.

29th Chromosome-Centric Human Proteome Project Workshop, 2024 Chromosome Team Anniversary

Wed, 29 Jan 2025 18:52:31 GMT

The 29th C-HPP Workshop was held on October 20 in Dresden, Germany. We acknowledged each of the chromosome teams' contributions and their recent reorganization and equalization of team leadership male-to-female ratios and now with ECR representation on each team. Commemorative plaques were presented to each of the chromosome team leaders, echoing the presentation of plaques in 2010 after the start of the CHPP.

HUPO ECR Committee Welcomes New Members

Wed, 29 Jan 2025 18:06:47 GMT

Maximilian Wulf

Max is a postdoctoral researcher at the Medizinisches Proteom-Center of the Ruhr-University Bochum and is involved in several research projects on the application of proteomic techniques (especially spatial and few cell proteomics) in neurobiological contexts. In his Ph.D. thesis, he investigated the proteome of neuromelanin granules in postmortem brain samples from donors with Parkinson's disease and dementia with Lewy bodies. Part of this work was awarded the "Wissenschaftspreis 2023" by the German Parkinson and Movement Disorders Society (Deutsche Gesellschaft für Parkinson und Bewegungsstörungen e.V.), which recognizes significant contributions to Parkinson's disease research by early-career researchers. In addition to his research interests, Max is passionate about teaching proteomics to undergraduate students, collaborating with other early-career researchers from different disciplines, and communicating advances in proteomics to a wider audience.

Ihor Arefiev

Ihor is an MSc student in Biochemistry at the University of Sherbrooke. His project is focused on finding evidence of non-canonical proteins translation in mouse testes. He is excited to become an active member of the HUPO ECR Committee and is eager to be involved in the organization of the HUPO World Congress.

Valeriia Vasylieva

Valeriia is an MSc student at Sherbrooke University in the MABLAB group. Their focus is on tackling challenges in discovering the noncanonical proteins. She recently started her journey in proteomics and is excited by the field. She is eager to contribute to the HUPO ECR Committee to give back to the community, gain transversal skills, and meet amazing people.

Call for the 2025 HUPO Early Career Researcher Manuscript Competition!

Wed, 29 Jan 2025 17:23:40 GMT

The HUPO Early Career Researcher (ECR) Committee is pleased to announce a call for the 11th anniversary of the ECR Manuscript Competition, sponsored by Taylor and Francis, at HUPO 2025 taking place November 9 - 13, in Toronto, Canada. The Manuscript Competition is a unique opportunity for early career researchers to gain visibility in the proteomics community, as it serves as a platform to highlight the invaluable contributions that postdoctoral fellows, young clinicians, and junior faculty members make to the proteomics field.

We encourage early career proteomics researchers to participate in this competition with an already published or accepted manuscript during the 2024 and 2025 calendar years. Three finalists will be selected to present their publications in a dedicated plenary session at HUPO 2025, where an expert committee will evaluate the oral presentations to determine the “Proteomics Highlight of the Year” by an ECR.

Eligibility criteria: This competition is intended for postdoctoral fellows (Ph.D. degree awarded post January 2019), junior faculty members (appointment post January 2021 and PhD awarded post January 2013), and young clinicians (M.D. degree awarded post January 2018). Applicants must be HUPO members. Career interruptions and leave, such as parental leave, will be considered to extend the eligibility period. Finalists from previous years are not eligible to participate.

Publication criteria: The applicant must have contributed significantly to the publication as the first or last (or shared first/last) author. The publication must be an original research article. Review articles will not be considered for this competition. The publication must have been accepted or printed for publication at the time of submission for the competition but must not have been published before January 1, 2024. Manuscripts that were posted on bioRxiv and other pre-print servers prior to submission will be considered.

How to Apply: A complete application must include the documents listed below. Send completed applications by email to ecr@hupo.org.

A single publication file as a pdf (including the supplementary information, if applicable) and

Single publication file as a pdf (including the supplementary information if it applies)

The manuscript must be an original research article, and the applicant must have contributed significantly to the concept and/or experimental work and/or data analysis (first, co-first, corresponding or co- corresponding author)
The publication must have been accepted and/or printed for publication at the time of submission to the competition, but not earlier than January 1, 2024.
The publication must be in English.

2. A short statement (300 words maximum) in which the applicant describes the novelty and impact of the publication on the field of proteomics.

Deadline to apply: March 28, 2025

HUPO ECR Events at HUPO 2025

Wed, 29 Jan 2025 16:27:30 GMT

Building on the success of HUPO 2024, the HUPO Early Career Researcher (ECR) Committee is eager to share our plans for HUPO 2025, which will take place November 9 - 13, in Toronto, Canada. We have put together a diverse programme of events and competitions to foster growth and connection within the community.

Here is what you can expect:

Manuscript & 3-Minute Thesis Competitions: Showcase your research and hone your communication skills.
Poster Competitions: A vibrant space to visually present your findings and engage with others.
Mentoring Sessions: Connect with experienced researchers for valuable guidance and support.
HPP Research Day
Rising Star Award: Celebrate outstanding early career research and recognize outstanding contributions.
ECR Networking Event: Build lasting connections with fellow researchers and explore potential collaborations.

We will be sharing more details on the HUPO 2025 website and in upcoming HUPOST newsletters. This program offers something for every ECR. Mark your calendars and join us for a year of learning, collaboration, and unforgettable experiences at HUPO 2025!

HUPOST January 2025

Wed, 15 Jan 2025 22:00:30 GMT

The January HUPOST is now available including the 2025 Congress Updates, News from ETC Committee & More

HUPO Education and Training Committee: Pre-Congress Training Course Summary

Wed, 08 Jan 2025 18:29:33 GMT

The HUPO Education and Training Committee (ETC) successfully organized precongress training courses during the HUPO Congress in Dresden 2024. We extend our heartfelt thanks to all the participants for contributing to the success of these sessions. The precongress training courses were well attended and provided valuable insights, helping participants deepen their knowledge of proteomics. If you have suggestions or recommendations for future training courses, please feel free to contact the ETC.

Summary of Session #1: Post-translation modification -insight into sample preparation, enrichment, detection, and computation.

This pre-congress training course was designed to address various aspects of posttranslational modifications (PTMs), offering insights into sample preparations, enrichment techniques, detection methods, and computational approaches for analyzing and profiling PTMs. The session aimed to educate and inspire researchers and students interested in measuring and understanding PTMs in biological or clinical samples.

The panelists for the session included esteemed experts in the field: Prof. Birgit Schilling (Buck Institute for Research on Aging, USA), Prof. Martin Larsen (University of Southern Denmark, Europe), and Prof. Daniel Kolarich (Griffith University, Australia). They provided in-depth coverage of different PTMs, including phosphorylation, glycosylation, cysteine modifications, and other modifications like malonylation and succinylation. Each expert shared the latest state-of-the-art tools and methodologies while highlighting future directions in PTM sample preparation and analysis.

The training course attracted many audience members, including graduates and early career researchers. Despite being the first session on day 0 of the HUPO Congress, it garnered significant attention and participation. Attendees provided overwhelmingly positive feedback, noting that it offered a comprehensive snapshot of various PTMs. They appreciated the opportunity for fruitful discussions with the panellists, which extended beyond the session into subsequent days of the conference. This interactive format enriched the learning experience and fostered valuable connections within the proteomics community.

The "Proteomics Essay Corner" is on. We have our first submission.

Wed, 08 Jan 2025 18:21:24 GMT

The Symphony of Proteomics

In the dance of life, proteins play,
With post-translational tunes on display.
Phosphorylation sparks their flame,
A phosphate touch to fuel the game.

Cysteine whispers, bonds anew,
Redox shifts, a path to pursue.
Modifications subtle, yet profound,
In these small marks, life is found.

Glycosylation, sugars sweet,
Chains of charm, functions meet.
Signal, structure, cell’s embrace,
Decorate the protein's face.

Succinylation, a mark so rare,
Metabolic threads it lays bare.
Histone trails and energy's crest,
A nuanced role in life's behest.

Proteomics, a map so vast,
Revealing secrets of the past.
Through every PTM, a story told,
In bonds of science, mysteries unfold.

We invite you to write essays or poems that explore and endorse the vast and fascinating landscape of proteomics and related fields.

How to Submit:

Please send your essays or poems to [Justyna.Fert-Bober@cshs.org; blandine.chazarin@gmail.com]. There is no due date, but we wish to share the work on a monthly basis. Feel free to include a title and a brief description of your work if you wish.

Let’s celebrate the -omics world together over coffee and creativity! We look forward to your submission and to enriching our community with your thoughts and inspirations.

HUPOST December 2024

Thu, 05 Dec 2024 16:22:18 GMT

The December HUPOST is now available including the 2025 Congress Updates, News from ECR Committee & More

ECR Committee Welcomes New Leadership

Mon, 02 Dec 2024 18:12:06 GMT

Welcome to the new members stepping in to lead the ECR efforts forward:

Co-chairs: Charlotte Hutchings and Livia Rosa
VC Logistics: Emily Hashimoto-Roth
VC Online Activities: Jessica del Castillo Alferez
VC Communications: Ireshyn Govender
HPP Delegates: Christian Moritz (B/D-HPP) and Dongxue Wang (C-HPP)

Keep reading to view their biographies:

Charlotte Hutchings

Charlotte is a final year PhD student in Prof. Kathryn Lilley's Group at the University of Cambridge. Her research currently focuses on the use of expression and subcellular spatial proteomics methods to explore the response of HEK293 cells to the production of viral vectors for gene therapy. Charlotte particularly enjoys the challenge of dealing with large datasets and has become an active member of the Bioconductor community, learning and teaching coding skills around the world as well as publishing multiple data analysis workflow to promote open research and analysis. She also sits on several committees, including the British Society for Proteome Research, HUPO Early Career Researchers and HUPO Marketing and Outreach committee. Charlotte is not only enthusiastic about her research, but is also interested in education, promoting equality in science and being a core member of the proteomics community.

Livia Rosa-Fernandes

Livia, D.Sc., is a Research Fellow in Neuroproteomics at the Macquarie Medical School's Motor Neuron Disease Research Centre. She earned her B.Sc. in Biomedical Sciences and M.Sc. in Biological Sciences with a focus on Genetics from the Federal University of Rio de Janeiro. Dr. Rosa-Fernandes completed her D.Sc. in Medical Sciences at the University of São Paulo Medical School, where she integrated molecular and cellular biology with quantitative proteomics to investigate multidrug resistance in chronic myeloid leukemia. During her postdoctoral research at the University of Southern Denmark, she expanded her expertise in systems biology, studying neurodevelopmental impairment caused by Zika Virus infection. Her current research focuses on the impact of aberrant protein interactions in the development of neurological pathologies. Dr. Rosa-Fernandes is a recipient of the Gilberto B. Domont Award, which honors young scientists' contributions to advancing proteomic sciences. She is member of the Brazilian Proteomics Society council and is engaged in several initiatives to promote knowledge transfer and increase access to scientific education.

Emily Hashimoto-Roth

Emily is a graduate student at the University of Toronto, Canada, pursuing a Ph.D. in Computational Biology and Molecular Genetics under the supervision of Dr. Hannes Röst. Her research aims to leverage mass spectrometry-based proteomics, lipidomics, metabolomics, and computational methods to better understand the onset and progression of gestational diabetes mellitus and future development of type II diabetes. Previously, she completed her M.Sc. in Biochemistry specializing in Bioinformatics at the University of Ottawa, Canada, under the co-supervision of Dr. Mathieu Lavallée-Adam and Dr. Steffany Bennett, where her research focused on the application of machine learning algorithms to mine and analyze protein-protein interaction datasets. Her passion for research, however, extends beyond the lab. Since 2020, she has also been a member of the Canadian National Proteomics Network and Human Proteome Organization, helping to strengthen the proteomics field by fostering welcoming communities for researchers of all career stages to meet and collaborate.

Jessica del Castillo Alferez

Jessica is a PhD candidate at Sanquin Research, Amsterdam and affiliated to University of Utrecht, Netherlands. She is part of the Symphony consortium, which aims to improve treatment for hemostatic disorders by addressing interindividual variations in bleeding tendencies. Her PhD research seeks to link the proteome to the bleeding phenotype by profiling plasma and blood cells to identify haemostasis modifiers. Her work focuses on proteomic profiling of patients to monitor response to treatment in bleeding disorders as well as applying plasma peptidomics to investigate fundamental aspects of haemostasis. Jessica is passionate about clinical proteomics, a field she entered during her master’s internship at the University of Groningen while studying proteomic adaptations in asymptomatic MCADD. Beyond her research, Jessica is an enthusiastic member of the HUPO ECR Committee since 2022 and has been actively involved in the organization of panel discussions and congress activities such as mentoring sessions and competitions. In her role as vice chair, she will contribute to the organization of panel sessions to provide a space for the proteomics community to come together and discuss important topics about navigating a career.

Ireshyn Govender

Ireshyn serves as a senior scientist at the Council for Scientific and Industrial Research (CSIR) in South Africa. He commenced his tenure at CSIR in 2013 as a candidate researcher, concentrating his efforts on clinical proteomics within the realm of precision medicine for HIV/AIDS. He earned his Ph.D. from the University of the Witwatersrand in 2019. Ireshyn is actively involved in clinical research groups that leverage proteomics to tackle diseases prevalent in South Africa and among underrepresented populations, focusing on the identification of prognostic and/or diagnostic protein biomarker panels. Additionally, he holds the position of vice-chairperson and is a member of the executive committee of the South African Association for Mass Spectrometry (SAAMS). In his new capacity as VC Communications of the HUPO ECR Committee, he aims to further highlight the exceptional contributions of early-career researchers and to enhance the connection between specialized scientific endeavours and the broader public.

Christian Moritz

Christian is a researcher at the University Hospital of Saint-Étienne, France. He did his PhD in the field of neuroproteomics in Kaiserslautern/Germany and moved to translational biomedical research for his postdoc projects in France. There, he is screening the human proteome for novel autoantigens targeted by serum antibodies of patients with rare neuropathies.

Dongxue Wang

Dongxue is currently an associate research professor at the National Center for Protein Sciences in Beijing (NCPSB) and the head of the mass spectrometry platform at the π-HuB Project Infrastructure in Guangzhou, China. She obtained her doctoral degree in proteomics in Dr. Bernhard Kuster's group at the Technical University of Munich. After that, she joined NCPSB in Beijing in 2019 and the π-HuB Project Infrastructure in Guangzhou in 2021. Dongxue has been focusing on developing and applying mass spectrometry-based proteomics technologies, integrating with clinical data and other omics, to understand human biology and diseases better. During her PhD, she and colleagues established the most comprehensive proteome and transcriptome atlas of 29 healthy human tissues, providing a protein expression baseline for examining human health and diseases. As a scientist at the National Center for Protein Science and the π-HuB Project Infrastructure, she and her team have been developing high-throughput and fully automated proteomics pipelines. They apply these methods in analyzing large cohorts of clinical samples to discover novel biomarkers and drug targets for nasopharyngeal cancer such as nasopharyngeal carcinoma, melanoma, lung adenocarcinoma, and polycystic ovary syndrome, among others. As a member of the HUPO community and the ECR committee, Dongxue looks forward to serving as a vital link and making valuable contributions to the activities of the ECR and HPP committees.

HUPOST November 2024

Tue, 12 Nov 2024 16:19:06 GMT

The November HUPOST is now available including the HUPO 2024 wrap-up & Photos, New HPP Portal, ECR Competition Award Winners, HUPO Election Results & More

3-Minute Thesis Competition: Big Ideas in a Short Time

Thu, 07 Nov 2024 19:39:39 GMT

Sponsored by Mass Dynamics

We had a very inspiring 3-minute thesis competition session, where 11 PhD students tackled the challenge of presenting their complex research projects in just three minutes, using only one static slide, as if addressing a lay audience. The creativity displayed was remarkable, with each student distilling intricate topics into accessible, engaging presentations that captivated the audience. Their precision in both timing and delivery reflected impressive skill and dedication.

The standout presentation came from Ericka Itang, who took us into a "proteomics crime scene".

Winner: Ericka Itang
Max-Planck-Institute of Biochemistry, Germany: Unlocking Clues to Childhood Illness: Exploring Proteins as Disease Markers

Runner-up: Linus Wollenweber
Utrecht University, Netherlands: The Odd One Out – Mass Spectrometric Detection of the Ever-Changing IgG4 Landscape

Runner-up: Julian Müller
Technical University Munich, Germany: PTMNavigator: Interactive Visualization of Differentially Regulated Post-Translational Modifications in Cellular Signaling Pathways

3-Minute Thesis Competition Sponsored By:

A Lively HUPO 2024 Poster Competition

Thu, 07 Nov 2024 19:02:00 GMT

Sponsored by Molecular Omics

Over the course of three days, the HUPO 2024 poster competition showcased the vibrant research diversity of our community. Thirty esteemed judges from various regions and scientific disciplines convened to evaluate the innovative work of our preselected student and postdoctoral finalists.

The presentations were assessed based on graphical elements, delivery skills, content richness, and overall impact. We extend our heartfelt congratulations to all the finalists. The overwhelmingly positive feedback from the judges underscores the exceptional caliber of the presentations, reflecting the cutting-edge research and dedication of the participants.

WINNERS

Postdoc
Thierry M. Nordmann

P-II-0644 A Proteomic Skin Disease Atlas for Accurate and Rapid AI-Driven Clinical Decision Making

Student
Sophia Steigerwald

P-II-0687 Single Cell Deep Visual Proteomics (scDVP) of Human Hepatocytes in Alpha-1 Antitrypsin Deficiency

RUNNERS-UP

Postdoc
Matthew The

P-II-0689 An End-to-End (phospho) Proteomics Data Analysis Platform for Precision Oncology of 1000 Prospective Pan-Cancer Patients

Postdoc
Fabian Frommelt

P-III-0880 Deep Interactome Profiling MS (DIP-MS), a Novel Interaction Proteomics Method for the Deconvolution of Immunoprecipitated Protein Complexes

Student (Master)
Adele Nel

P-II-064 Comparative Proteomic Analysis of Breast Cancer and Normal Tissues with Deep Plasma Profiling using the Mag-Net™ Workflow

Student
Tilman Werner

P-II-0704 Proteomic Profiling of IDH-Wildtype Glioblastoma Reveals Prognostic Subtypes with Matching Abundances of Semi-Specific Peptides in Serum

Poster Competition Sponsored by:

Early Career Researchers Put on a Show at the Manuscript Competition: Proteomics Highlight of the Year Session during HUPO 2024

Thu, 07 Nov 2024 18:49:42 GMT

Sponsored by Expert Review of Proteomics Taylor and Francis

The annual HUPO Early Career Research Manuscript Competition was run by the HUPO ECR Committee in collaboration with YPIC. Over 25 manuscripts were submitted to be reviewed by three external reviewers. At the HUPO 2024 World Congress, attendees were invited to watch the three finalists present their groundbreaking proteomics research in a plenary session sponsored by Expert Review of Proteomics by Taylor & Francis.

All three speakers gave exciting talks and eventually a panel of judges crowned Stacy Malaker’s paper entitled “Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE” as the Proteomics Highlight of the Year. Stacy was awarded a cash prize of $1,000 USD and the two fabulous runner’s up, Marc van Oostrum and Leyuan Li, received cash prizes of $500 USD each.

The HUPO ECR Committee and YPIC would like to thank all of the reviewers and in-person judges who facilitated this competition to run so smoothly. Additional thanks go to all of the Early Career Researchers who submitted a manuscript. Stay tuned for next year’s manuscript competition submissions for HUPO 2025 in Toronto, Canada.

Winner

Dr. Stacy Malaker Department of Chemistry, Yale University: Glycoproteomic Landscape and Structural Dynamics of TIM Family Immune Checkpoints Enabled by Mucinase SmE

Runner-Up

Dr. Marc van Oostrum University of Basel: The Proteomic Landscape of Synaptic Diversity Across Brain Regions and Cell Types

Runner-Up

Dr. Leyuan Li National Center for Protein Sciences, Beijing: Revealing Proteome-Level Functional Redundancy in the Human Gut Microbiome using Ultra-Deep Metaproteomic

Manuscript Competition Sponsored by:

Missed the Mentoring Sessions at HUPO? We Have You Covered!

Thu, 07 Nov 2024 14:55:41 GMT

The ECR Mentoring Sessions provide a space for mentors and mentees to come together and openly discuss relevant topics about navigating an early career.

These sessions highlighted the importance of opening a dialogue about the many factors that influence our careers. Thank you to all the speakers listed below for their honest advice and to the many early career researchers who attended and took the opportunity to ask questions!

Mental Health: Building resilience to manage work and job search stress
Chairs:

Ireshyn Govender (Council for Scientific and Industrial Research, South Africa, ZA)
Martha Ingola (Bayer AG, Preclinical Development, Germany, DE)

Speakers:

Jennifer Geddes-McAlister (University of Guelph)
Stuart Cordwell (The University of Sydney)
Adriana Franco Paes Leme (Brazilian Biosciences National Laboratory)

The mental health mentoring session at HUPO 2024 shed light on the importance of managing one’s mental health throughout their scientific journey. Presentations showed an intimate look into the personal experiences of the three speakers which were well received by everyone, including senior researchers and ECRs.

The speakers all shared valuable tips for maintaining a positive outlook especially in the light of rejection which is a common occurrence in the scientific world. Listening to their experiences brought a sense of comfort knowing that rejection happens to everyone and it is not personal.

Finally, the panel discussion afforded attendees an opportunity to directly engage with the panelists. A wide array of questions were posed from participants at different career stages.

This led to fruitful discussions where the panelists and other attendees shared their thoughts and advice.

Mastering mentorship: Navigating conflicts and personalities
Chairs:

Livia Rosa-Fernandes (Centre for Motor Neuron Disease Research, Sydney / AU)
Daniel Garama (Monash University, Melbourne / AU)

Speakers:

Dr. Blandine Chazarin (Postdoctoral Scientist at PRISM laboratory, France)
Dr. Chiara Francavilla, (Associate Professor at DTU Bioengineering, and an honorary Senior Research Fellow, University of Manchester)
Dr. Parag Mallick (Associate Professor at Stanford University and Chief Scientist at Nautilus Biotechnology, a next-generation proteomics company)

The mentoring session "Mastering Mentorship: Navigating Conflicts and Personalities," was a captivating convergence of professionals from diverse geographical regions and various career stages in both industry and academia.

The session provided a platform for speakers to share their career paths and the significant impact of conflict situations on their professional growth.

Attendees gained insights into the characteristics of challenging personalities and acquired strategies to manage, mitigate, and resolve conflicts effectively. A common thread among the concerns shared by attendees was the profound effect of difficult situations on career progression and mental health, including the potential loss of employment or projects, and the pervasive influence of a toxic work environment on the overall group dynamics.

The diverse backgrounds of the speakers contributed to a nuanced discussion about the attendees' worries, which included navigating jealousy and favoritism, as well as other detrimental dynamics that can be often found well-established in research groups.

Moreover, the session delved into the essential qualities of effective leadership and set expectations for the mentor-mentee relationship. The speakers maintained a positive outlook on conflict resolution, advocating for the expression of concerns in a respectful and considerate manner as the initial step towards addressing challenging scenarios. They also emphasized the importance of being open to constructive criticism and recognizing one's role within the dynamics of the relationship.

Career Paths: What’s Next in Your Career?
Chairs:

Jessica Del Castillo (Sanquin, Utrecht University, Amsterdam, NL)
Christian Moritz (University Hospital CHU of Saint-Étienne, FR)

Speakers:

Christoph Krisp (Application Development Specialist Proteomics at Bruker Daltonics, DE)
Maurine Fucito (Application Specialist at Evosep, DK, and President of the Young Proteomics Investigators Club)
Uli Ohmayer (Co-founder and Head of Mass Spectrometry at NEOsphere Biotechnologies, DE)
John Yates (Editor-in-Chief, Journal of Proteome Research, and Professor at the Scripps Research Institute, US)

The Career Paths: What’s Next in Your Career? session kicked off HUPO 2024 with Early Career Researchers eager to hear firsthand insights from experienced professionals across academia and industry. Speakers shared valuable lessons from their own career journeys, discussing essential moments and strategies that helped shape their paths.

The speakers emphasized the importance of self-reflection to understand one's goals, the role of networking to build professional relationships, and the added value of international experience in today’s globalized scientific landscape.

During the lively panel discussion, attendees asked pressing questions, including practical advice for those who find networking challenging—particularly for introverts.

The session concluded with an interactive “standing table” format, where attendees gathered around their preferred speakers for small-group discussions. This allowed for deeper conversations and immediate networking training. The informal setting stimulated open dialogue and practical advice. A big thank you to all the speakers and attendees who contributed to making this mentoring session a source of inspiration and practical guidance!

ETC Webinar Series September 9th, 2024: Dr. Philip Remeš

Wed, 06 Nov 2024 18:02:31 GMT

“The Past, Present and Future of Quadruple Ion Trap Mass Spectrometers in Proteomics”

Dr. Philip Remeš, a Senior Research Scientist at Thermo Fisher Scientific, presented an educational seminar on ion trap mass spectrometers. In addition to discussing how ion traps work fundamentally, Dr. Remeš covered the strengths and weaknesses of ion traps for proteomics, as well as how ion traps are likely to be used for proteomics in the near future. Approximately 50 participants were in attendance.

Ion traps have played a critical role in the birth of mass spectrometry-based proteomics. He began by tracing the historical development of ion traps, starting from their invention in the 1950s by Wolfgang Paul. Initially used in physics to manipulate ions, ion traps were later adapted for mass spectrometry, with significant improvements made by George Stafford and colleagues in the 1970s and 1980s that enhanced their efficiency and suitability for proteomics applications. From a historical perspective, Dr. Remeš highlighted the gradual increase of ion utility with ion traps relative to triple quadrupole mass spectrometers in commercial instruments. He discussed how linear ion traps have improved upon earlier 3D designs and how linear traps have changed throughout the last quarter century.

Dr. Remeš discussed the evolution of data acquisition technologies in proteomics, emphasizing the transition from qualitative analyses using data-dependent acquisition (DDA) to more quantitative approaches like data-independent acquisition (DIA) and parallel reaction monitoring (PRM). He explained that while DDA, often coupled with Tandem Mass Tags (TMT) for sample multiplexing, is effective for peptide identification, it faces quantitation challenges due to interference. DIA has emerged as a powerful method that enhances throughput and coverage by simultaneously acquiring data on all ions and generating extensive peptide lists. He then highlighted that advancements in ion trap technology have made PRM highly effective for quantitative proteomics. He pointed out that ion traps can now achieve quantitation performance comparable to, or even surpassing, that of Orbitraps and time-of-flight mass spectrometers, especially in targeted assays, thus broadening their applicability in modern proteomics workflows.

Several criticisms of ion trap usage in proteomics have been waged. In particular, ion traps have markedly lower mass resolution than Orbitraps or time-of-flight (ToF) mass spectrometers. Dr. Remeš emphasized that this lower mass accuracy is still generally sufficient for proteomics applications. Since peptides produce multiple fragment ions during mass spectrometry, a sufficient number of fragment ions generally remain interference-free even with low mass resolution. With technological advancements like automatic gain control (AGC) and the integration of deep learning tools that predict peptide fragmentation patterns, ion traps have become highly quantitative, even at low input levels. Therefore, despite their inherent limitations in mass accuracy, ion traps remain valuable and effective instruments in the field of proteomics due to their sensitivity, efficiency, and the sufficiency of their resolution for most proteomic analyses.

This session included an extended Q&A session with the audience, guided by Brian Searle (Ohio State University, USA). A full video recording of the session, including the Q&A session, is available on the HUPO Proteomics Webinars and Virtual Presentations website (https://hupo.org/Webinars-and-Virtual-Presentations).If you haven’t had the chance yet, please check out the webinar. Share it with your colleagues, coworkers, or friends.
Cheers!

Creation of the HPP Portal – A Knowledge Hub to Support the HPP Grand Challenge

Mon, 04 Nov 2024 18:26:15 GMT

During the years, the scientists from the entire world, especially the ones involved in the Human Proteome Project (HPP) have accumulated massive knowledge on human proteins. Since 2012, the advance of the Chromosome-centric HPP (C-HPP) defined stringent criteria of protein existence. All of this information was collected in the neXtProt database. It became a valuable resource of human protein research. In 2023, a mirror site of neXtProt was established by Chi-Biotech in Shenzhen, China, facilitating the access from Asian countries.

In 2024, the neXtProt database was discontinued. Therefore, a new HUPO-branded knowledgebase, named HPP Portal, is under construction by the team of Dr. Gong Zhang (Jinan University, China) and Chi-Biotech.

The HPP Portal aimed to continue the idea of neXtProt, cataloging the knowledges to each human protein. It contains the information to UniProt, Human Protein Atlas, etc., and includes the Protein Evidence (PE) levels. A notable change is that the annotation is now based on GENCODE. This facilitates the connection to the genome and transcriptome data, and reduces the inconsistency when processing multiomics datasets. In addition, Function Evidence (FE) levels of each protein is provided, summarizing the current knowledge on protein functions. For those proteins without known functions, the predicted functions will be also included. The HPP Portal, fully HUPO and HPP branded, is the knowledge hub supporting the HPP Grand Challenge.

Fun Under the African Sun - Ubuntu Proteomics Summer School

Mon, 04 Nov 2024 17:48:08 GMT

Are you tired of the lack of sun during the northern hemisphere winter and looking to learn more about proteomics at one of the most well-received sun-soaked proteomics summer schools currently available? The Ubuntu Proteomics Summer School brings together an amazing list of speakers for our third event, being held in February 2025 in Durban, South Africa.

Join us and listen to talks from the likes of Jesper Olsen, Bernhard Küster, Kathryn Lilley and more (see full program here).

The Ubuntu Proteomics Summer School (UPSS) is a one week residential school with a concepts and applications track. The summer school aims to help researchers:

Learn more about proteomics from leading experts in the field
Connect to new networks, and create collaborative opportunities
Explore new and dynamic locations (the summer school is a “floating” one and consequently changes location each year)
Grow capacity to advance proteomics driven research in multiple fields

Explore galleries from the 2023 and 2024 schools, view the YouTu be channel, X and LinkedIn profiles.

If you are interested in attending, please apply here, or spread the word to any interested parties.

#ubuntuproteomics

OBO the UPSS organizing committee

Introducing the Proteomics Essay Corner!

Mon, 04 Nov 2024 17:22:56 GMT

Attention HUPO Members!
We are excited to announce a special opportunity for all members to showcase their creativity and passion for the -omics world through our " Proteomics Essay Corner." We invite you to write essays or poems that explore and endorse the vast and fascinating landscape of proteomics and related fields.

Submission Guidelines:
Length: It is up to author; however, we would encourage to not go over 1000 words.

Anonymity: You may submit your work anonymously if you prefer.

Content: Your piece can reflect personal experiences, insights into the -omics revolution, or creative interpretations of the impact of proteomics on science and society.

This initiative is not only a chance to express your thoughts but also to foster a sense of community among HUPO members who share a passion for the ever-evolving -omics world. Whether you’re a seasoned researcher or a budding enthusiast, we encourage your unique voice to be heard!

Why Participate?
Share Your Perspective: Engage with fellow members and contribute to the discourse surrounding proteomics.

Inspire Others: Your words might inspire others to delve deeper into -omics research and applications.

Visibility: Selected submissions will be featured in our upcoming newsletter and online platforms, providing you with a chance to reach a broader audience.

How to Submit: Please send your essays or poems to [Justyna.Fert-Bober@cshs.org; blandine.chazarin@gmail.com]. There is no due date, but we wish to share the work on monthly basis. Feel free to include a title and a brief description of your work if you wish.

Let’s celebrate the -omics world together over coffee and creativity! We look forward to your submissions and to enriching our community with your thoughts and inspirations.

Happy writing!
For more information about the -omics field and recent advancements, check out resources available on the HUPO website or other scientific platforms.

HUPOST October 2024

Wed, 02 Oct 2024 23:02:54 GMT

The October HUPOST is now available! Chock full of the latest HUPO 2024 news, finalists and info about the upcoming ECR events, the C-HPP Workshop, career opportunities and more!

Spotlight on the Proteomics Highlights of the Year

Wed, 02 Oct 2024 20:42:03 GMT

Sponsored by Expert Review of Proteomics Taylor and Francis

The Proteomics Highlights of the Year plenary session at HUPO 2024 will take place on Monday, October 21st at 17:45 in the Plenary Hall at the International Congress Center Dresden. This exciting session features the finalists from the ECR Manuscript Competition, who will present some of the most innovative recent work in proteomics from emerging scientists. We are thrilled to introduce the three finalists who will present their cutting-edge research in a plenary session:

Stacy Malaker (Yale University, USA); view Stacy's bio here.
Marc van Oostrum (Max Planck Institute for Brain Research, Germany); view Marc's bio here.
Leyuan Li (Beijing Proteome Research Center, CN); view Leyuan's bio here

The winner of the competition will be determined based on their oral presentation, and will take home $1,000; runners-up will be awarded $500.

This week, we are shining a light on our last, but certainly not least, finalist, Leyuan Li, who will present her manuscript entitled: “Revealing proteome-level functional redundancy in human gut microbiome using ultra-deep metaproteomics.” Her research focuses on using metaproteomics and other advanced techniques to unravel the complexities of our internal microbial ecology. Take a look hereat her short bio.

Calling All Proteomics Contributors: Share your Story!

Wed, 02 Oct 2024 20:32:38 GMT

The proteomics community is a vibrant and dynamic group of scientists, researchers, and professionals, all bound by a shared passion for understanding the complexities of proteins. As part of the HUPO community, we know that proteomics isn't just a field of study - it's a global network of collaboration, innovation, and discovery. What makes you love being a part of this amazing community?

HUPO wants to hear from you! Whether it’s the groundbreaking research, the collaborative spirit, or the sense of belonging, your story can inspire others and highlight the incredible diversity of experiences within HUPO. Submit your personal reflections or professional anecdotes and help us highlight some very special moments in the proteomics community. We’re going to feature them in the HUPO booth (looping video presentation) at HUPO 2024 in Dresden!

Ruth Huttenhain, Assistant Professor, Stanford: “I love HUPO because it unites a vibrant and diverse community of scientists who share a passion for exploring protein function.”

Mathieu Lavallée-Adam, Associate Professor, University of Ottawa: "The HUPO World Congress is where I found my postdoctoral job! Networking within HUPO has helped me build new collaborations and friendships."

Send your short stories (and photo) to office@hupo.org by October 11. Help us celebrate what makes HUPO an exceptional community for proteomics professionals worldwide!

Notice of HUPO General Assembly of Members (GAM)

Wed, 02 Oct 2024 20:20:27 GMT

The 2024 General Assembly of Members (GAM) will be held during HUPO 2024 in Dresden, Germany just prior to the Awards Ceremony and Closing Session:

Date: Wednesday, October 23, 2024
Time: 1615-1645 (local Time)
Location: Plenary Hall, International Congress Center Dresden

HUPO members are invited to attend for important HUPO updates and networking. Contact the HUPO Office (office@hupo.org) for more information.

UniProt Actively Supporting the HPP Grand Challenge

Wed, 02 Oct 2024 15:29:53 GMT

neXtProt has not been updated since October 2023 and solutions are being sought to revive this major database. In the meantime, the resource remains available for users at both nextprot.org and nextprot.cn with a very large number of visitors each month.

To support the HPP as they move forward, UniProt has taken on the role of running the Proteomics Identification pipeline. This has involved upgrading existing UniProt MS peptide identification pipeline to meet the stringency of the HPP3.0 guidelines, and working with Eric Deutsch (PeptideAtlas) and Nuno Bandeira (MassIVE) to ensure all additional criteria for data evaluation are met.

UniProt release 2024_04 shows that 18,417 proteins now have PE1 level evidence, out of a total of 19,835 candidate entries (93%). The data will be visible in the UniProt Feature Viewer and accessible via an API and a full analysis will be published in the 2024 report on the proteome from the HUPO Human Proteome Project, currently in preparation. UniProt has long supported the data generated using HUPO Proteomics Standards Initiative data standards.

In addition to the peptide pipelines, we are working with Eric Deutsch, Andy Jones (U. Liverpool) and Juan Antonio Vizcaino (EMBL-EBI) to use deposited MS data to identify additional high-confidence PTM sites and these will be added to UniProt human protein records over the next few months. Protein interactions and complexes generated by the IMEx databases are already accessible through our records. The UniProt database is committed to supporting the HUPO HPP with its next Grand Challenge of identifying a function for every human protein and looks forward to a closer working relationship with this group in the future.

Join the ECR Mentoring Sessions at HUPO 2024!

Wed, 02 Oct 2024 15:26:12 GMT

The HUPO ECR Mentoring Sessions provide a space for mentors and mentees to come together and openly discuss relevant topics on navigating an early career in proteomics. Three insightful sessions will take place at HUPO 2024 in Dresden, Germany with the following mentors and topics:

Career Paths: What’s Next in Your Career? (Sunday, Oct. 20, 14:15 - Conference Room 3-4)

John R. Yates III (Scripps Research)
Christoph Krisp (Bruker Daltonics GmbH & Co. KG)
Maurine Fucito (Evosep)
Uli Ohmayer (NEOsphere Biotechnologies GmbH)

Mental Health: Building Resilience to Manage Work and Job Search Stress (Tuesday, Oct. 22, 15:15 - Conference Room 3-4)

Stuart Cordwell (University of Sydney)
Jennifer Geddes-McAlister (University of Guelph)
Adriana Franco Paes Leme (Brazilian Biosciences National Laboratory)

Mastering Mentorship: Navigating Conflicts and Personalities (Wednesday, Oct. 23, 15:00 - Conference Room 3-4)

Chiara Francavilla (Danish Technical University)
Parag Mallick (Stanford University)
Blandine Chazarin (PRISM laboratory)

These sessions are designed to foster lively discussions and offer practical advice to help you navigate your career. Don't miss the opportunity to learn and ask your questions to experienced mentors and connect with peers facing similar challenges!

C-HPP Workshop Program

Fri, 27 Sep 2024 19:20:41 GMT

C-HPP Workshop
Sunday, October 20th, 2024
Seminar Room 7, International Congress Center Dresden, Germany

Session One: C-HPP Update and Business Meeting (Chair, Chris Overall)

9:00: Welcome, C-HPP Annual Report and Update (Chris Overall)
“Gender and Geographic Diversity in the C-HPP and Team Renewal.”

9:30: Elections for C-HPP EC positions vacant: We welcome nominations from the floor or by email prior to the Workshop.

(a) Chair 2025-2028 (Nominations: Gong Zhang; )
(b) Co-Chair (if Gong Zhang is elected Chair, a Co-Chair position becomes vacant. If so, nominations for the Co-chair: Fernando Corrales; )
(c) Secretary General (Nominations Heeyoun Hwang; ) (if Heeyoun Hwang is elected Secretary General, a Co-Chair position becomes vacant. If so, nominations for the CoChair: Josh Labaer; )
(d) Member-at-large (Nominations Gilberto Domont; )
(e) ECR Member (Nominations from HUPO ECR Committee)

9:45: ECR Talk “Discovery of a Novel Player in ER-Mitochondria Interactions by DARTS-LC-MS/MS Proteomics Analysis” (Minjeong Ko, Korea)

10:00: "Unlocking the Secrets of Chromosome 2: The Critical Role of Associated Proteins in Health and Disease – Now a Danish Contribution” (Allan Stensballe + Louise Bundgaard)

10:15-10:45: Biobreak/Coffee

Session Two: C-HPP Team Updates (Chair Gong Zhang)

10:45: Mitochondria team: “Humanin-Like Peptides” (Viviana Greco)

11:00: ECR talk “TMEM160, a Protein Belonging to Chromosome 19 with no Assigned Function, Promotes Tumoral Growth in Non-small Cell Lung and Cervical Cancer Cell Lines” (Gloria Angelina Herrera-Quiterio)

11:15: Chr 20 Team China “An Enquiry Towards the Identification Criteria of Missing Proteins” (Yuxin Li)

11:30: "Celebrating 10 Years of the C-HPP with a Regrouping Ceremony and Plaque Presentations” (Heeyoun Hwang + Chris Overall)

12:00-12:30: Working Lunch

Session Three: Functionalization of PTMs and Proteins (Chair Ho Jeong Kwon)

12:30: “The HPP Portal (HP3) Compiling GO + HPA + Uniprot” (Gong Zhang)

12:50: “FE Classification Update” (Eric Deutsch)

13:10: “GO Consortium and the C-HPP” (Pascale Gaudet)

13:20: General Discussion

14:00: Workshop Close

20:00: C-HPP Workshop Dinner

ECR is delighted to showcase the finalists of the 10th edition of the annual manuscript competition.

Fri, 27 Sep 2024 19:05:51 GMT

Dr. Leyuan Li is one of the three finalists selected to present their manuscripts during the manuscript competition in a dedicated plenary session at HUPO2024. Their talks will be evaluated by a panel of experts to select the “Proteomics Highlight of the Year”. Dr. Leyuan Li will be presenting her work: "Revealing proteome-level functional redundancy in human gut microbiome using ultra-deep metaproteomics.”

Dr. Leyuan Li is currently a Junior Principal Investigator at the National Center for Protein Sciences (Beijing), also known as the Phoenix Center. From 2016 to 2022, she was a postdoctoral fellow and research associate at Dr. Daniel Figeys’s lab at the University of Ottawa. Her training included developing in vitro culturing techniques and automating metaproteomics for rapidly assessing personalized microbiome drug responses. In 2022, she started-up the Proteome-level Microbial Systems Ecology (ProMiSE) Lab at the Phoenix Center. Her new endeavor focuses on using metaproteomics and other advanced techniques to unravel the complexities of our internal microbial ecology. Her research aims to provide deeper insights into the ecology and functions of microbial communities within the human body for future personalized interventions.

Meet the Finalists for the 2024 Poster Competition

Fri, 27 Sep 2024 18:55:49 GMT

Congratulations to the finalists of the 2024 Poster Competition for both the Postdoctoral and the Graduate Student Category.

Postdoctoral Category:

Anna Pagotto, ETH Zurich
Enes Ugur Max Planck Institute of Biochemistry
Fabian Frommelt CeMM
Heather Murray The University of Newcastle
Hsiang-En Hsu Academia Sinica
Jan N. Hansen Stanford University
Jonas P. Becker German Cancer Research Center
Magdalena Kuras Lund University
Malte Sielaff University Medical Center of the Johannes Gutenberg-University Mainz
Matthew The TU Munich
Rebecca Herzog Medical University of Vienna
Thierry M. Nordmann Max Planck Insitutue of Biochemistry
Tristan Cardon INSERM U1192 Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM)
Vishnu Mohan Weizmann Insitute of Science
Yaoting Sun Westlake University

Graduate Student Category:

Adele Nel University of Pretoria
Aigerim Kassym Jena University hospital
Alicia-Sophie Schebesta Max Planck Institute of Biochemistry
Alireza Nameni VIB-UGent
Amy George Newcastle University
Jan Simonik Masaryk University
Johannes P. Zimmermann Univeristy of Würzburg
Julian Müller Technical University of Munich
Lucas Rodrigues-Ribeiro National Institute of Science and Technology in Nanobiopharmaceutics
Maximilian Zwiebel MPI of Biochemistry
Melissa S Vorster Stellenbosch University
Nicolai Bjødstrup Palstrøm Odense University Hospital
Pinar Altiner Institute of Pharmacology and Structural Biology (IPBS)
Sophia Steigerwald Max Planck Institute of Biochemistry
Tilman Werner University Medical Center Freiburg
Vivien Wiltzsch Fraunhofer Institute for Cell Therapy and Immunology
Yan Zhou Westlake University

HUPOST September 2024

Thu, 05 Sep 2024 20:06:36 GMT

The September HUPOST is now available! Have a look at the latest HUPO 2024 updates, news from the HBPP, webinars from ETC and ECR, new job ads and other exciting info on upcoming HUPO activities.

Meet the 2024 Finalists for the 3-Minute Thesis Competition

Tue, 03 Sep 2024 22:45:53 GMT

Congratulations to the following PhD candidates who will be presenting their research in just 3 minutes during HUPO 2024 world congress in Dresden!

Alireza Nameni
I am currently a third-year PhD student at VIB-UGent Belgium, with a background in artificial intelligence and engineering. My research includes various projects with a primary focus on iDeepLC, a deep learning-based retention time predictor for modified peptides, and the Mokapot project, which enhances peptide-spectrum match identification using nonlinear machine learning algorithms.

Johanna Wallner
Hi there, I am Johanna. I studied Biochemistry at TU Munich and developed a passion for proteomics towards the end of my master's studies. This led me to pursue a PhD at OmicScouts GmbH, a company specializing in proteomics-based research. I am also affiliated with the Sieber Chair at TU Munich. The project I will present here is a collaboration with the Bundeswehr Institute of Microbiology. Our goal is to develop an easy-to-use model system for studying a variety of viral infections.

Julian Müller
Hi! I'm Julian, a PhD student at the Chair of Proteomics and Bioanalytics at TUM, Germany. I'm a bioinformatician by training and fell in love with proteomics during my masters, so you will find me either at a PC or in front of a mass spec. My PhD project revolves around cellular signaling cascades, particularly those involving phosphorylation. Our group uses phosphoproteomics and kinase inhibitors to study these signaling cascades, and my job is to write software that facilitates the analysis and interpretation of these large datasets.

Julia Schessner
After studying molecular biotechnology at the University of Heidelberg for my Bachelor's and Master's degree I returned to my hometown Munich and started my PhD at the Max-Planck-Institute of Biochemistry. Throughout my studies I always worked in the wet-lab, as well as the dry-lab, writing data analysis tools for the data I acquired myself. This was a perfect fit for my work on the subcellular organization of the proteome, where I needed to use all my skills from cell culture to data analysis to drive my projects. What grounds me is my 2 year-old daughter who I hope to inspire to always follow her curiosity and to never stop learning.

Carmen Garcia Duran
I am a PhD student in the Department of Microbiology and Parasitology at Complutense University of Madrid under the supervision of Dr Concha Gil. My research focuses on the study of microbiota in disease using metaproteomics, with special interest in sepsis and long-COVID. The main objective is to gain a deeper understanding of these communities and identify disease biomarkers, such as microbial proteins or microorganisms.

Ericka Itang
Ericka Itang is a third-year PhD student at the Max Planck Institute of Biochemistry in Martinsried, Germany. She has developed a workflow that combines dimethyl-based labeling and sample multiplexing with data-independent acquisition, known as multiplexed-DIA (mDIA). Recently, she applied this mDIA workflow to the proteomics analysis of clinical samples such as urine and plasma to map the landscape of pediatric health and disease. Her research interests also include investigating the role of endogenous peptides in therapeutics. Born and raised in the Philippines, Ericka moved to Germany in 2021 to further her education and expand her horizons in scientific research.

Yu Zong
I am a PhD student from Fudan University, Shanghai, China. My research interest involves applying artificial intelligence to solve important questions in proteomics. My main work focuses on predicting phosphopeptides and glycopeptides spectra using advanced deep learning models.

Shaufa Shareef
As a final-year PhD student, I am researching biomarker discovery for infectious diseases such as COVID-19, and investigating the mechanistic basis of immune responses to such conditions. I am a biochemist by training, with a focus on clinical biochemistry and the relationship between scientific discovery and how that translates to clinical practice. I grew up in Maldives, studied in the UK, and have worked in various aspects of the Maldivian health sector. As such, I also have a keen interest in health inequalities and the disproportionate effect of infectious diseases in this context. I look forward to gaining more insights in the field during HuPo 2024.

Linus Wollenweber
Linus is a second year PhD student in Albert Heck's lab at Utrecht University. Coming from a background in Molecular Biotechnology, he is working on the mass spectrometric analysis of intact Antibody fragments (Fabs). He is currently expanding the toolbox required to measure antibodies from human specimen with clonal resolution. This requires method development in sample preparation, purification, and work on appropriate LC-MS methods to analyze the complex samples.

Robbe Devreese
I am a first-year PhD student in the CompOmics group at the VIB-UGent Center for Medical Biotechnology in Ghent, Belgium. My research focuses on enhancing the prediction of collisional cross-sections of peptides in ion mobility-assisted LC/MS-MS. The aim of my PhD project is to utilize these improved predictions for more sensitive and specific analysis of (clinical) DIA proteomics data.

Annica Preikschat
My name is Annica Preikschat, I graduated from Friedrich Alexander University Erlangen in the field of immunology and I am now working at AG Tenzer in the Core facility of proteomics in the Institute of Immunology at the Unimedical Center of Mainz. My PhD is supported by the Transmed Training program and connects both, immunology and mass spectrometry. The project aims to identify peptides which are important for the adaptive immune response in rheumatoid arthritis patients. This will help to better characterize arthritis and might result in the development of a treatment.

Dominik Lux
Dominik Lux is a computer scientist pursuing his PhD in Bioscience at the Medical Proteome Center, Ruhr-University Bochum, Germany. He focuses on unidentified mass spectrometry data by incorporating besides well-known protein sequences, mutations, variants, and more. By utilizing graphs and established methods, he aims to identify such entries. His PhD research focuses on gaining a deeper understanding of Parkinson's disease, though his approach and tools can be broadly applied.

Daniel Flender
Daniel Flender is a PhD candidate at the University of Antwerp and the Flemish Institute for Technological Research ( VITO), specializing in immunopeptidomics in non small cell lung cancer (NSCLC). His research aims to identify and analyze peptide antigens, with the goal of developing targeted immunotherapies and advancing cancer treatment strategies. By uncovering specific peptides that can trigger immune responses, Daniel's work aims to enhance the precision and effectiveness of cancer treatments. His contributions are pivotal in advancing our understanding of immune system interactions with cancer, ultimately striving to improve patient outcomes and innovate therapeutic approaches in oncology.

ECR Delighted to Showcase the Finalists of the 10th Edition of the Annual Manuscript Competition

Tue, 03 Sep 2024 22:39:11 GMT

Dr. Marc van Oostrum is one of the three finalists selected to present their manuscripts during the manuscript competition in a dedicated plenary session at HUPO2024. Their talks will be evaluated by a panel of experts to select the “Proteomics Highlight of the Year”. Dr. Marc van Oostrum will be presenting his work: The proteomic landscape of synaptic diversity across brain regions and cell types.

Dr. Marc van Oostrum is currently an SNSF Ambizione Junior Group Leader in Prof. Peter Scheiffele’s laboratory at the Biozentrum of the University of Basel. His research focuses on employing spatial proteomics to unravel the molecular organization and diversity of neuronal synapses. Marc completed his Master’s in Biochemistry at ETH Zürich, where he conducted his thesis research in Prof. Paola Picotti’s lab. He pursued his PhD at the Institute for Molecular Systems Biology at ETH Zürich under Prof. Bernd Wollscheid, specializing in cell surface and spatial proteomics. His postdoctoral work, carried out in Prof. Erin Schuman’s lab at the Max Planck Institute for Brain Research in Frankfurt am Main, explored the molecular diversity of synapses.

News from the HUPO Human Brain Proteome Project (HBPP)

Tue, 03 Sep 2024 22:03:00 GMT

The 33^rd HBPP Workshop took place from May 22^nd to 24^th 2024, in Naas, just outside Dublin, in Ireland. It was a very successful, small but intense meeting with participants from Australia, Brazil, Germany, Ireland, Saudi Arabia, Sweden, United Kingdom, and the USA.

The meeting addressed clinical, animal, and cellular findings for neurodegeneration (e.g. Alzheimer’s disease, Parkinson’s disease, Multiple Sclerosis) and neuropsychiatric conditions such as Schizophrenia, Bipolar disorder and Autism. Whilst most of the work presented employed mass spectrometry-based proteomics, there was a trend of employing large-scale protein arrays of different kinds as well as combination of proteomics with other –omics platforms. Advanced statistical analyses including multivariate machine learning as well as Mendelian randomization of GWAS findings were elegantly combined with proteomics findings. Pathway analyses and investigations of posttranslational modifications were also presented.

Christopher Whelan from Johnson and Johnson presented an update from the findings of the open-access proteomics resource profiling on blood plasma samples collected from over 50,000 UK Biobank participants to elucidate the biological mechanisms underlying proteo-genomic discoveries (Nature. 2023 Oct;622(7982):329-338. doi: 10.1038/s41586-023-06592-6. Epub 2023 Oct 4.PMID: 37794186.).

In addition, we welcomed PreOmics at the meeting to display their latest products. We also discussed lab sustainability actions and accreditation (My Green Lab).

There was ample time for networking at the meeting, and it was exciting to hear about related lab exchanges that are ongoing and planned.

The discussions and continuing work done by HBPP is significant and helps to advance the development and roll out of neuroproteomic methods to acquire holistic insights of the brain proteome in health and disease.

The 34th HUPO HBPP workshop will take place in Toledo, USA, in 2025. Further details will be announced on the HBPP website https://hupo.org/Brain and https://x.com/BrainProteomics in due course.

For more information regarding this workshop or the Human Brain Proteome Project, please visit the HUPO website here and/or contact: Melanie Föcking (mfocking@rcsi.ie, current chair of HBPP) or Darragh O’Brien (darragh.obrien@ndm.ox.ac.uk, HBPP communications officer).

HUPOST August 2024

Tue, 06 Aug 2024 18:26:09 GMT

The August HUPOST is out now! It’s chock-full of news and updates including the 2024 HUPO Awardees, Call for HUPO Executive Committee nominations, Slate of 2024 HUPO Council nominees, Congress updates, ETC and ECR activities, and more!

ECR Delighted to Showcase the Finalists of the 10th Edition of the Annual Manuscript Competition

Mon, 29 Jul 2024 19:43:41 GMT

Stacy Malaker is one of the three finalists selected to present their manuscripts during the manuscript competition in a dedicated plenary session at HUPO2024. A panel of experts will evaluate their talks to select the “Proteomics Highlight of the Year”. Stacy Malaker will be presenting her work: Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE.

Dr. Malaker is an Assistant Professor in the Department of Chemistry at Yale University. Her laboratory is focused on establishing methods and technology to study mucins, a class of densely O-glycosylated extracellular proteins, by mass spectrometry. Additionally, the laboratory studies mucins in a biological context, since these proteins play integral, yet poorly understood, roles in numerous diseases. Prior to her appointment at Yale, she received her B.S. from the University of Michigan in Biochemistry and Anthropology-Zoology. Dr. Malaker then went on to receive her PhD in Chemistry from the University of Virginia in the laboratory of Professor Donald Hunt. She continued to investigate the role of aberrant glycosylation in cancer as an NIH postdoctoral fellow in Professor Carolyn Bertozzi’s laboratory at Stanford University before starting at Yale in 2021.

News from C-HPP

Wed, 03 Jul 2024 17:51:53 GMT

Chromosome Team Leadership
Good news: Drs. Allan Stensballe and Louise Bundgaard, both excellent scientists, will lead the Chromosome 2 team representing Denmark. Now all our chromosomes have a team!!!

C-HPP Workshops
Upcoming workshops for 2024 and 2025:

26^th C-HPP Workshop: (0.5 day), Dresden, Sunday 20^th October 2024, 9:00 AM – 14:00 PM (before HUPO Congress).
27^th C-HPP Workshop on the new Human Proteome Project Portal, Guangzhou LEDY Life and Health City, China, November 28 & 29th 2024.
28^th C-HPP Workshop: The HPP Grand Challenge, Saint-Malo, France, June 13-15, 2025 (before EUPA).

Elections in Dresden for C-HPP EC Members
Please send nominations for the following positions to the C-HPP Secretary General, Dr Peter Horvatovich (p.l.horvatovich@rug.nl).

Chris Overall will be stepping down as Chair of the C-HPP at the end of 2024, and we invite nominations for the new Chair.
Gilberto Domont is a current member, and we invite nominations to fill this position for three years starting in January 2025.
C-HPP Secretary General Dr Peter Horvatovich will be stepping down at the end of 2024, and we invite nominations to fill this position for three years starting in January 2025.
We are creating a new ECR position for the C-HPP EC, and we will elect in Dresden a new ECR to sit on the EC from January 2025 for 3 years. Please self nominate.
Election for a member-at-large of the C-HPP EC for three years starting in January 2025.

Our goal is to have equal female and male representation on the C-HPP EC.

Current C-HPP EC

Christopher M. Overall, Canada (to December 31, 2024), Chair.
Gong Zhang, China (to December 31, 2027), Co-Chair.
Heeyoun Hwang, Korea (to December 31, 2028), Co-Chair.
Peter Horvatovich, The Netherlands (to December 31, 2025), Secretary General.
Gilberto Domont, Brazil (to December 31, 2024), Member-at-Large.
Fernando Corrales, Spain (to December 31, 2025), Member-at-Large.
Sergio Encarnación-Guevara, Mexico (to December 31, 2027), Member-at-Large.

Sydney International Conference: Advancing Multi-Omics into the Clinic

Wed, 03 Jul 2024 17:32:08 GMT

November 18-19, 2024
Location: Aerial UTS Function Centre, Ultimo, Sydney, Australia
Organized By: Children Medical Research Institute, ProCan

Through this two-day meeting, internationally renowned experts in proteomics, genomics, cancer management, biomarker and drug discovery will share their progress towards addressing the challenges and opportunities of multi-omic data integration in cancer management, with a special focus on the role of proteomics in advancing biomarker development and drug discovery.

More details here....

Join Us for the HUPO Early Career Researchers Networking Evening at HUPO 2024 World Congress in Dresden, Germany!

Wed, 26 Jun 2024 22:57:31 GMT

Sunday, October 20th 19:30-22:30

Early career researchers and senior scientists are all welcome to join this exciting event, which aims to bridge digital, cultural, and continental gaps. The ECR Networking Evening provides a fantastic opportunity for early-stage researchers to meet, share, and connect with colleagues and senior researchers.

This year, the evening will feature a scenic boat ride around Dresden, offering stunning views, drinks, and a chance to mingle in a relaxed atmosphere. It's the perfect setting to network with peers and mentors from around the world.

Be ready to meet new people and participate in engaging activities!

Congratulations to the finalists of the Manuscript competition!

Wed, 26 Jun 2024 22:56:11 GMT

The manuscript competition is a unique opportunity for early career researchers to gain visibility in the proteomics community, as it serves as a platform to highlight the important contributions that postdoctoral fellows, young clinicians and junior faculty members make to the proteomics field. Three finalists have been selected to present their publications in a dedicated plenary session at HUPO 2024, where an expert committee will evaluate the oral presentations to determine the “Proteomics Highlight of the Year” by an ECR. Congratulations to all finalists:

Leyuan Li (Beijing Proteome Research Center, CN)- Revealing proteome-level functional redundancy in human gut microbiome using ultra-deep metaproteomics
Stacy Malaker (Yale University, USA) - Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE
Marc van Oostrum (Max Planck Institute for Brain Research, Germany.) - The proteomic landscape of synaptic diversity across brain regions and cell types

HUPOST June 2024

Tue, 04 Jun 2024 18:13:24 GMT

The June HUPOST edition is out now! It’s packed with vital news and updates, including information on HUPO 2024 the IAB Spotlight, Council Elections, New Job Postings, ETC and ECR Activities, and more!

Remarkable HUPO Volunteers - Marketing & Outreach Committee (MOC)

Thu, 30 May 2024 22:18:49 GMT

In this new monthly feature, we will be highlighting extraordinary HUPO volunteers who lead and support many of HUPO's various Committees, Initiatives and Working Groups. If you would like to volunteer with HUPO, please connect with the HUPO Office.

HUPO Marketing and Outreach Committee (MOC)

The MOC has been at work developing new ways to promote the HUPO mission, the visibility of proteomics within the scientific community and its popularization among the public, as well as gathering funding support. The MOC has been very successful in networking with other HUPO Committees and Initiatives and using a range of tools and activities. The MOC members are from different fields and backgrounds and at various career stages representing the diversity of HUPO.

Charlotte Hutchings is a third-year PhD student at the Cambridge Centre for Proteomics, University of Cambridge. She applies expression and subcellular spatial proteomics methods to study the effect of viral production, specifically that of adeno-associated viruses, on cells. Charlotte is also very interested in bioinformatics and big data which has led her to write and teach workflow publications and workshops. Having found a love for proteomics, Charlotte has become an active member of the community and acts as the student representative for the British Society for Proteome Research (BSPR), Vice Chair of Online Activities for the HUPO Early Career Researcher (ECR) Committee and has more recently become involved in the HUPO Marketing and Outreach (MOC) Committee.

Theodora Katsila is a Senior Researcher-Head of the Biomarker Discovery & Translational Research laboratory at the National Hellenic Research Foundation, Greece. Craving for brain teasers (and being loyal to her motto: from information to actionable insights), she is strongly interested in translational biomarkers and proteoform-based drug repurposing. Mining the chemical biology space, Theodora aims to catalyze the transition from serendipity-driven to data-driven translational precision medicine. This paradigm shift comes with a need for biomarker-guided trial design and patient-centric companion diagnostics. For this, Theodora applies mass spectrometry-based multi-omics and data science.

Conor McCafferty is a Program Manager at the Murdoch Children’s Research Institute in Melbourne, Australia, where he coordinates and oversees the body of cancer research performed at the institute and the adjoining Royal Children’s Hospital. He has worked with proteomic technologies to investigate biomarkers of disease and completed his PhD investigating the relationship between thrombosis and COVID-19 in children from the University of Melbourne in 2022, which included proteomic analysis of patients with different COVID-19 outcomes. Conor joined the HUPO Marketing and Outreach Committee in 2019 and additionally sits as a board director of the Australian Society for Medical Research. He has a passion for solving clinical challenges (particularly in pediatrics) and works to develop coordinated research and multi-omic strategies to improve clinical outcomes.

iMOP Webinar: Exploring New Model Organisms and Unraveling Protein Mysteries

Mon, 06 May 2024 16:42:22 GMT

The Initiative for Model Organism Proteomics (iMOP) unveils an exciting webinar titled "Exploring New Model Organisms and Unraveling Protein Mysteries."

Mark your calendars for May 21st and get ready to explore the world of proteomics and learn how it's revolutionizing our understanding of molecular mechanisms in a range of new model organisms. Join them on this journey as they shed light on how these discoveries can boost human health, safeguard the environment, and preserve biodiversity. See further webinar details on the flyer below.

Zoom Meeting Link Here

Remarkable HUPO Volunteers - Marketing & Outreach Committee (MOC)

Tue, 30 Apr 2024 00:01:24 GMT

In a new feature of the monthly HUPOST newsletter, extraordinary HUPO volunteers who lead and support many of HUPO's various Committees, Initiatives and Working Groups, are highlighted. If you would like to volunteer with HUPO, please connect with the HUPO Office.

HUPO Marketing and Outreach Committee (MOC)
The MOC has been at work developing new ways to promote the HUPO mission, the visibility of proteomics within the scientific community and its popularization among the public, as well as gathering funding support. MOC members are from different fields and backgrounds and at various career stages representing the diversity of HUPO.

The May HUPOST features the following MOC volunteers:

Qian Zhao is an Associate Professor at the Hong Kong Polytechnic University (HK PolyU). She received her Ph.D. in Chemistry from the University of Hong Kong in 2012 and then joined the University of California, San Francisco (UCSF) as a postdoctoral researcher. In 2017, she joined HK PolyU as an Assistant Professor in Chemical Proteomics. She currently serves as an Editorial Board member for Molecular & Cellular Proteomics and a council member in HUPO. Her research group investigates functional peptides with mass spectrometry, including non-canonical peptides translated from small open reading frames and immunopeptides. Qian holds the view that the peptidome, a subset of the proteome, holds significant promise. Her work is centered around creating new ways to find and understand these peptides, with the ultimate aim of using their potential to develop new treatments for diseases.

Nobuaki Takemori is a Senior Assistant Professor at Ehime University. He received his B.Sc. degree in Material Science in 1997 from Nagoya Institute of Technology (Japan) and his Ph.D. degree in Material Science in 2002 from Japan Advanced Institute of Science and Technology (Japan). After postdoctoral research from 2002 to 2009 in the US and Japan, he joined the faculty at Ehime University as a Research Assistant Professor in 2010 and was promoted to Senior Assistant Professor with tenure in 2012. He is currently a Council Member of the Human Proteome Organization (HUPO) and the Japanese Proteomics Society (JPrOS) and serves as the Chief Editor of Proteome Letters, the official journal of JPrOS.

His research group is focused on developing new proteomics technologies and their application to clinical biomarker discovery. In his own laboratory, he has developed an innovative method for the synthesis of stable isotope-labeled proteins using a wheat germ cell-free protein synthesis system in addition to establishing a high-throughput synthesis platform. Awarded the Young Investigator Award from JPrOS in 2018 for his pioneering work in the development of quantitative proteomics technologies using a wheat germ cell-free synthesis system, his technique has been extremely useful for the production of high-quality internal standard proteins in the quantitative analysis of targeted proteins by mass spectrometry, resulting in a unique impact in the field of quantitative proteomics. In recent years, he has also been actively engaged in the development of sample preparation techniques for top-down proteomics. He has successfully developed PEPPI-MS, a high-resolution fractionation technique for intact proteoforms using SDS-PAGE, and is now conducting research on top-down proteomics at high depth by combining PEPPI-MS with an ultra-high resolution mass spectrometry system.

Upendra Chalise is a postdoctoral fellow at Dr. Jop van Berlo's lab in the University of Minnesota, where he studies cardiovascular physiology after sterile cardiac injury such as myocardial infarction and transaortic constriction in murine model. He uses cellular and plasma proteomics techniques to identify markers that can predict future progression of cardiac remodeling. His graduate work has utilized various proteomic approaches in identifying and validation potential markers and functional targets to improve cardiac outcomes after myocardial infarction. He has continued his work in his postdoctoral training in modulating inflammatory and extracellular matrix proteins to prevent adverse cardiac remodeling and heart failure progression. He is actively working to regulate immune responses after cardiac injury through identification of protein targets. Upendra currently serves as a member of the HUPO Marketing and Outreach Committee and in the Trainee Advisory Sub Committee of the Cardiovascular section of the American Physiological Society. Besides cardiovascular research, Upendra is passionate about improving academia for trainees and actively advocates for changes within academia.

Deadline Approaching for the Rising Star Award Nomination !

Thu, 25 Apr 2024 03:53:36 GMT

This early career achievement award seeks to honor early career researchers who have had an exceptional impact on the proteomics field and community. This impact can take the shape of publications, patents obtained, development of a commercial product, establishment of a symposium, workshop, course, training program or any other meaningful contributions or service to the field of proteomics. The winner of the award will give a short presentation during the closing ceremony of HUPO 2024 and take home a cash prize of $2000. To participate, candidates can self-nominate or be nominated. Click here to learn more about how to apply, eligibility criteria, and prizes.

SUBMISSION DEADLINE: May 10th, 2024

Last chance to Submit your Abstract and Participate in the Poster Competition at HUPO 2024 in Dresden SUBMISSION DEADLINE: May 31st, 2024

Thu, 25 Apr 2024 03:49:00 GMT

Get ready to put your research in the spotlight at HUPO 2024 with our exciting poster competition sponsored by Molecular Omics! To participate, simply indicate your interest in the competition when submitting your abstract. It's as easy as checking a box!

Fifteen outstanding abstracts from graduate students and postdocs will be selected as

finalists, based on the quality of their abstracts. These finalists will have the opportunity to present their posters during the conference, where they'll be evaluated by a jury of experts. Winners in both categories (graduate students and postdocs) will each receive a cash prize of USD$200, while four runners-up will be awarded USD$100.

As a bonus, submitted abstracts have the opportunity to be selected for a short talk at the day of the research initiatives. This is your chance to showcase your research findings, innovative methodologies, and exciting discoveries to a global audience!

Submit your abstract here today!

Final Call: Share Your Ph.D. Thesis in Three Minutes! SUBMISSION DEADLINE: May 31st, 2024

Thu, 25 Apr 2024 03:43:32 GMT

Can you condense your thesis in three minutes? Join us at the 3-Minute Thesis Competition, in collaboration with the HUPO Early Career Researcher (ECR) Committee and the Human Proteome Project (HPP). Presenting your thesis allows you to highlight the significance and impact of your research.

To participate submit a lay abstract through the HUPO 2024 abstract submission portal . Craft your abstract without scientific jargon, ensuring it's easily understood by a general, non-expert audience.

Finalists will be selected based on their abstracts to present their thesis topic, using a single static slide during a session at HUPO 2024.

This competition provides an opportunity for you to present your work in a brief but engaging format, fostering discussions and collaborations with fellow researchers from around the world.

Let your creativity shine as you describe your thesis research topic in 300 words or less!

The inside scoop: Navigating the 3MT with HUPO’s 2023 winners

Wed, 17 Apr 2024 23:12:30 GMT

DATE: Thursday, April 25, 2024
TIME: 4 am PDT/ 7 am EDT/ 1 pm CEST
SPEAKERS: Dina Schuster (Utrecht University), Janaina Silva (University of Sao Paulo), Yun-Jung Yang (Taipei Medical University).

REGISTER HERE

Webinar Description: During this event, the three winners of the 2023 3-Minute Thesis Competition will present their thesis in a more detailed format, share their experiences from the competition, and provide some advice for future participants. After the presentations, there will be a Q&A session. If you are interested in participating in this year's 3-Minute Thesis Competition at the congress, be sure to attend this webinar.

REGISTER HERE

After registering, you will receive a confirmation email containing information about joining the webinar.

33rd Human Proteome Organization Brain Proteomics Project Workshop in Ireland

Tue, 16 Apr 2024 16:09:42 GMT

We are thrilled to invite you to the 33rd workshop of the Human Proteome Organization (HUPO) Brain Proteomics Project. This exciting event will bring together leading researchers, scientists, and experts from around the world to discuss groundbreaking advancements in the field of brain proteomics.

CONFERENCE DETAILS:

DATE: May 22-24, 2024
LOCATION: Lawlor's of Naas, Poplar Square, Naas, Co. Kildare, Ireland

REGISTER HERE

CONFERENCE HIGHLIGHTS: The meeting program focuses on alternative and transformative frameworks for understanding CNS disorders and the use of enhanced and newly emerging tools for experimental measurement and manipulation. Presenters will share research techniques and experimental designs they applied to elucidate the biological pathways and markers associated with psychiatric and neurodegenerative symptoms and CNS disorders.

CUTTING-EDGE RESEARCH: Explore the latest discoveries and innovations in brain proteomics, including the identification and characterization of proteins crucial to understanding brain function and diseases.

Our speakers are internationally recognized experts. We have keynote speakers and several unique sessions covering hot topics on functional proteomics, biofluidomics, plus our sessions on ad-vances in neurodegenerative disorders and neuroproteomics in drug discovery and development.

KEYNOTE SPEAKERS: Engage with renowned scientists who have made significant contributions to the field of proteomics and brain research.

CONFIRMED SPEAKERS:

Dr. Chris Whelan, Director, Neuroscience, Data Science & Digital Health, Janssen Research & Development, LLC and lead of the collaboration and corresponding author of the Nature paper sharing preliminary findings from the UK Biobank Pharma Proteomics Project (UKB-PPP, Nature 2023; 622(7982): 329–338.PMID:37794186)
Prof. Robert McCullumsmith, Department Chair at The University of Toledo, College of Medicine and Life Sciences
Prof. Daniel Martins-de Souza, Associate Professor and Head of Proteomics, Dept of Biochemistry, University of Campinas (UNICAMP)
Prof. Katrin Marcus, Medical Proteome Analysis, Center for Proteindiagnostics (PRODI), Ruhr-University Bochum

NETWORKING OPPORTUNITIES: Connect with fellow researchers, build new collaborations, and strengthen your professional network.

CALL FOR ABSTRACTS: We welcome abstract submissions on a wide range of topics related to brain proteomics, including but not limited to:

Biofluidomics
Neurodegenerative Diseases
Neuropsychiatric Disorders
Biomarker Discovery
Neuroproteomics in drug discovery and development

Please submit your abstract by April 30, 2024

REGISTRATION INFORMATION: For registration and additional details, please visit our conference website: https://hbpp2024.sciencesconf.org/

Join us in advancing the field of brain proteomics and unravelling the mysteries of the human brain. We look forward to your participation in this landmark event.

HUPOST April 2024

Tue, 02 Apr 2024 21:32:53 GMT

The April HUPOST edition is now available.....filled with important news and information including HUPO 2024 congress updates, upcoming ETC webinars and ECR competitions, summer internship opportunities, IAB Member (CIL, Inc.) and volunteer spotlights, the CPTAC Survey, MCP's new Editor-in-Chief....and much more!

Summer Internship in Proteomics (SIP) 2024

Tue, 02 Apr 2024 18:51:44 GMT

Explore the world of proteomics, multi-omics and big data sciences through the Summer Internship in Proteomics (SIP) 2024 -- 1, 2 or 3 month internship opportunities available! Following the overwhelming response from students after the "Advances in Proteomics Technologies (APT)-2024 Workshop and Conference", the Summer Internship in Proteomics (SIP)-2024 is scheduled to take place from May 1st to July 31st, 2024. This program will feature a hybrid approach, incorporating online lectures, demonstrations, and data analysis, with brief laboratory activities at IIT Bombay-SINE, focusing on sample preparation and instrumentation.

See detailed descriptions here

For more information contact: proteomicasine@gmail.com

Join the WhatsApp group for more info: https://chat.whatsapp.com/Ddg8K92gjNZGPIFHoet5dq

REGISTER HERE

If You Missed the Last ECR Online Panel on ‘How to Get Recognized for Your Work'....We've Got You Covered!

Mon, 25 Mar 2024 18:17:30 GMT

Perseverance and passion are essential ingredients for success but how do you demonstrate that you have them? Our last panel discussion featured Dr. Laurent Gatto (Associate Professor of Bioinformatics, UCLouvain), Dr. Stacy Malaker (Assistant Professor of Chemistry, Yale University), and Dr. Juan Antonio Vizcaino (Scientist and Team Leader, Proteomics, European Molecular Biology Laboratory), who shared insights into managing important career steps and building a successful career in science. Key takeaways included the importance of showcasing expertise beyond academic output, such as public code contributions and collaborative projects. Also, focus on honing technical skills relevant to your projects, and don't underestimate the value of teamwork and collaboration. Networking plays a crucial role, not only in promoting your work, through conferences, social media, or online platforms like GitHub; but it can also be fundamental for leveraging opportunities for professional growth. You can watch this and other webinars here ; you can also read Dr Laurent Gatto’s notes here.

Submit Your Abstract and Participate in the Poster Competition at HUPO 2024 in Dresden

Mon, 25 Mar 2024 18:13:41 GMT

Abstract Submission is Open!

Calling all graduate students and postdocs to participate in the exciting poster competition at HUPO 2024 sponsored by Molecular Omics! To apply, simply indicate your interest in the competition when submitting your abstract. Check the box, and you're in the running!

Fifteen outstanding abstracts from graduate students and postdocs will be chosen as finalists, based on their quality. These finalists will have the chance to present their posters during the conference, where they'll be evaluated by a jury. Winners in both categories (graduate students and postdocs) will each receive a cash prize of USD$200, while four runner-ups will be awarded USD$100. Showcase your research and win!

Sponsored By:

Can You Share Your Ph.D. Thesis in Just Three Minutes?

Mon, 25 Mar 2024 18:00:15 GMT

Join us at the renowned 3-Minute Thesis Competition, in collaboration with the HUPO Early Career Researcher (ECR) Committee and the Human Proteome Project (HPP). This event offers phd students to showcase their innovative research in a focused, fast and fun session!

We're inviting all Ph.D. students to participate by submitting a lay abstract through the HUPO 2024 abstract submission portal. Craft your abstract without scientific jargon, ensuring it's easily understood by a general, non-expert audience. Let your creativity shine as you describe your thesis research topic in 300 words or less!

Finalists will be selected based on the quality of their abstracts. Participants will present their thesis topic, using a single static slide, and in a format that's accessible to everyone They'll have the chance to compete in the ultimate showdown during a session at HUPO 2024 in Dresden, Germany, from October 20-24. Are you up for the challenge?

Last Chance to Apply for the HUPO 2024 Early Career Researcher Manuscript Competition! Deadline April 15th!

Mon, 25 Mar 2024 17:55:57 GMT

Have you recently published in the field of proteomics? The 10th HUPO Early Career Researcher Manuscript Competition invites you to submit your manuscript for consideration at HUPO 2024 in Dresden, Germany, held from October 20-24. This prestigious competition is open to postdoctoral fellows, young clinicians, and junior faculty members eager to showcase their contributions to the proteomics community.

Submit your manuscript, published during the 2023 and 2024 calendar years, and compete for the coveted title of "Proteomics Highlight of the Year." Three finalists will be selected to present their work in a dedicated plenary session at HUPO 2024. This can truly be a once in a lifetime experience! Read about the experience from past participants (Dr. Johannes Bruno Müller-Reif, Dr. Pavel Sinitcyn and Dr. Hong Wang)!

The winner will receive a grand prize of $1,000 USD, while two runner-ups will each be awarded $500 USD. Don't miss your chance to shine and gain recognition for your outstanding research. Submit your manuscript before the deadline and mark your place in proteomics history!

This is your last chance to apply - Submit your application TODAY!

ETC Webinar Series: Fully Automated Proteomics Sample Preparation Applied to Chemical Proteomics and Plasma Proteomics

Wed, 20 Mar 2024 22:20:27 GMT

DATE: Wednesday, April 24, 2024
TIME: 7 am PST / 10 am EST/ / 3 pm CET
SPEAKER: Dr. Ruijun Tian

REGISTER HERE

Webinar Description: Are you excited by the latest mass spectrometers, such as Astral and Ultra? Wondering how to prepare your samples efficiently to maximize their capabilities? Join us for an insightful webinar hosted by the Education and Training Committee.

Speaker Bio: Dr. Ruijun Tian is a tenured professor in the Department of Chemistry at SUSTech. He serves as the director of the Research Center for Chemical Biology and Omics Analysis, SUSTech and vice president of CNHUPO. He received the National Science Fund for Distinguished Young Scholars. In 2008, Dr. Tian obtained his Ph.D. in Analytical Chemistry from the Dalian Institute of Chemical Physics, Chinese Academy of Sciences. In the same year, he joined the Institute for Systems Biology in Ottawa, Canada, for postdoctoral training. In 2010, he continued his postdoctoral research at the University of Toronto and Mount Sinai Hospital in Canada, supported by the Canadian Institutes of Health Research (CIHR) Postdoctoral Fellowship. In 2014, he was appointed as an Associate Professor in the Department of Chemistry at SUSTech and was promoted to a tenured Full Professor in 2020. His research focuses on proteomics related method development, as well as their applications in biomedical fields such as cell signaling and tumor microenvironment. He has published over a hundred papers in internationally renowned academic journals, including Nature, Nat. Chem. Biol., Cell Chem. Biol., Nat. Commun., PNAS, Mol. Cell. Proteomics, Anal. Chem.

REGISTER HERE

After registering, you will receive a confirmation email containing information about joining the webinar.

HUPOST March 2024

Tue, 05 Mar 2024 14:49:41 GMT

Read the lastest issue of the HUPOST containing exciting HUPO 2024 Info, IAB Member Spotlight, ECR Activities, ETC Webinars and much more!

Submit Your Abstract and Participate in the Poster Competition at HUPO 2024

Mon, 04 Mar 2024 14:56:52 GMT

The HUPO Early Career Researcher (ECR) Committee is excited to present this year’s Poster Competition sponsored by Molecular Omics. All graduate students (Master’s and PhD), as well as postdocs, are invited to participate in the HUPO 2024 poster competition taking place October 20-24, 2024 in Dresden, Germany.

To participate...graduate students and postdocs simply need to indicate in their abstract submission that they would like to participate in the competition. Fifteen abstracts from graduate students and fifteen abstracts from postdocs will be selected as finalists based on their quality.

Posters will be evaluated during the conference by a jury. Winners in both categories (graduate students and postdocs) will each receive a cash prize of $200 USD and four runner-ups will each receive $100 USD thanks to Molecular Omics. All early career proteomics researchers are invited to participate!

All early career proteomics researchers are invited to participate

The 3-Minute Thesis Competition Returns at HUPO 2024

Mon, 04 Mar 2024 14:51:48 GMT

Building on the success of previous 3-Minute Thesis Competitions, the HUPO Early Career Researcher (ECR) Committee and the Human Proteome Project (HPP) team up once again to provide this engaging competition. Present your proteomics Ph.D. thesis topic in 3 minutes using a single static slide and in a format that can be understood by a general audience.

To participate, simply submit a lay abstract via the HUPO 2024 abstract submission portal without scientific jargon that describes your Ph.D. thesis research topic. Abstract text should not exceed 300 words. Entrants must be enrolled in a Ph.D. program.

Finalists who will be selected based on the quality of their abstracts, will have the exciting opportunity to compete in the final showdown, to be held during a dedicated session at HUPO 2024 in Dresden, Germany (October 20-24). Are you up for the challenge?

Apply for the HUPO 2024 Early Career Researcher Manuscript Competition

Mon, 04 Mar 2024 14:44:33 GMT

Seize the opportunity to showcase your recent achievements in the dynamic field of proteomics! We invite early career researchers to apply for the 10th edition of the HUPO Early Career Researcher (ECR) Manuscript Competition, taking place at the HUPO 2024 World Congress in Dresden, Germany, October 20-24. This competition offers a unique platform for postdoctoral fellows, young clinicians, and junior faculty members to gain visibility within the proteomics community, emphasizing their significant contributions to the field.

Three finalists will be selected to present their manuscript (published during the 2023 and 2024 calendar years), in an exclusive plenary session at HUPO 2024, where an expert committee will evaluate the oral presentations to determine the "Proteomics Highlight of the Year." The first-place winner will receive a cash prize of $1,000 USD, while two runner-ups will each be awarded $500 USD.

Don't miss this chance to showcase your proteomics expertise and be recognized among peers at HUPO 2024!

Unsure about applying? https://www.hupo.org/News/13322997Hear from last year’s finalist here, Dr. Pavel Sinitcyn about his experience at HUPO 2023 in Busan, South Korea.

More information and details here about the competition, eligibility and how to submit on the HUPO website.

Deadline to Apply: April 1, 2024

Interview with 2023 HUPO ECR Manuscript Competition Finalist: Dr. Pavel Sinitcyn

Fri, 01 Mar 2024 09:22:04 GMT

Dr. Pavel Sinitcyn
Morgridge Institute For Research, United States

Pavel Sinitcyn is a distinguished Morgridge Interdisciplinary Postdoctoral Fellow at University of Wisconsin-Madison, conducting cutting-edge research in Dr.Joshua Coon’s lab. With a strong background in developing software solutions for proteomics data processing, Dr. Sinitcyn has played a pivotal role in developing tools such as MaxQuant, MaxDIA, Perseus, and Deep Proteomic Sequencing Methods.

Dr. Pavel Sinitcyn was a finalist in the HUPO 2023 ECR Manuscript Competition, for which he presented his manuscript, “Global Detection of Human Variants and Isoforms by Deep Proteome Sequencing”, in a plenary session. To get the inside story, we asked Dr. Sinitcyn a few questions about his experience in the competition. Read what he had to say below!

1. What is your current position and affiliation?
I am a postdoctoral researcher in the Coon lab at University of Wisconsin-Madison, United States. In June 2024, I will be starting my own group at Utrecht University in The Netherlands

2. How would you like your work to contribute to the field of proteomics?
I would like to see a change in the definition of protein coverage in the field. Rather than merely discussing protein coverage as the number of detected proteins out of the many annotated protein-coding genes, we should consider coverage as the portion of amino acids covered by a few detected peptides. This shift will enable a more comprehensive quantitative measurement of sequence isoforms, small amino acid variations, and post-translational modifications on a global scale.

3. What have you found in the HUPO community/congress?
I greatly appreciate the international mindset of the HUPO community. This conference goes beyond the opportunity to listen to great talks/posters and meet colleagues and friends in one place; it allows for the exploration of the landscape of the field on a global scale, spanning various countries and regions.

4. How was your experience/what did it mean to present your work at HUPO?
I thoroughly enjoyed my experience presenting my work at HUPO, especially within the HUPO ECR community. Returning to HUPO is always a pleasure. The conference's well-tuned schedule and scale allowed for a comprehensive experience without the usual need to constantly choose between simultaneous must-visit sessions. The vibrant atmosphere of the poster session and bioinformatics hub added to the overall positive experience. And finally, attending this conference was particularly meaningful for me as it was the first one after the birth of my son, giving me the opportunity to fully participate in the session organized by Moms in Proteomics.

HUPOST February 2024

Tue, 06 Feb 2024 13:41:34 GMT

Check out the latest edition of the HUPOST featuring HUPO 2024 Program, ECR Manuscript Competition and Online Panel, ETC Webinar Series, Upcoming Events and much more

Early Career Researcher Online Panel: Getting Recognised for your Work

Wed, 31 Jan 2024 17:28:56 GMT

Date: Wednesday February 28, 2024
Time: 4pm GMT (5pm CET)

Are you a Ph.D. student, postdoc, or early career researcher looking to get recognised for your work? Join the next HUPO Early Career Researcher online panel discussion, "Getting recognised for your work", at 4pm GMT (5pm CET) on Wednesday February 28.

The panel will feature Dr. Laurent Gatto (Associate Professor of Bioinformatics, UCLouvain), Dr. Stacy Malaker (Assistant Professor of Chemistry, Yale University), and Dr. Juan Antonio Vizcaino (Scientist and Team Leader, Proteomics, European Molecular Biology Laboratory).

This will be the perfect opportunity to ask any questions that you may have about getting recognised for your work and putting yourself in a favourable position for your future career.

REGISTER HERE

C-HPP Workshop on “Characterizing the Building Blocks of the Human Proteome”

Wed, 31 Jan 2024 16:51:38 GMT

The C-HPP is holding a workshop Madrid, Spain, at the National Center for Biotechnology, CSIC, Campus of the University Autónoma of Madrid, Darwin, 3, Spain.

A workshop hotel is being organized where registrants can book and cover their own accommodation. The hotel will be near the train station for a short 15-minute ride to the University Autónoma.

Registration and most meals and coffee are free and we invite members of the C-HPP, B/D-HPP, and HPP to register as soon as possible to help with planning.

REGISTER HERE

AGENDA

Wednesday, April 24

13:00-14:30 Welcome Lunch

Preworkshop Working Group on Protein Identification and Function Guidelines
(Chairs: Rob Moritiz + Charles Pineau)

14:30 – 16:30: Discussion on guidelines for (i) assigning protein function for the Grand Challenge, incorporating, (ii) With HUPO’s loss of support from neXtprot, also to be discussed will be a new repository for HPP progress on completing the Human Proteome Project and where the data will reside for functional annotation of the Human Proteome, (iii) SWATH/DIA data into the HPP.

16:30 Coffee

17:00 Finalize recommendations and action items on the three aims.

18:00 Dinner ad hoc in central Madrid, Tapas!

Thursday, April 25

Session One: Grand Challenge (Chairs Charles Pineau + Fernando Corrales)

9:00 Chris Overall. Welcome and outline of workshop.

9:15 Charles Pineau. C-HPP in Le Grand Challenge: (20 min + 10 mins)

9:45 General Discussion on the Grand Challenge and HPP Database Management

11:00 Coffee break

11:30 Gong Zhang(20 min + 10 mins): “Proteome-wide Functional Annotation Using Deep-Learning-based Protein Structures”.

12:00 Uwe Volker. Discussion Summary: Challenges in the Grand Challenge. (20 min + 10 mins)

12:30 - 14:00 Lunch

Session Two: Mission of the C-HPP (Chairs: Gong Zhang + Heeyoun Hwang)

14:00 Chris Overall. Outline of the C-HPP Mission Statement.

14:15 – 15:15 General Discussion on the C-HPP Mission Aims. Including gender and geographic diversity in the leadership of teams and EC, inactive teams/team renewal.

15:15 Yong-In Kim (Chr 9) (ECR) (15 min + 5 min): “Exploring Uncharacterized Proteins on Chromosome 9: Current Progress and Insight”

15:35 Alejandra Delgado (ECR) (15 min + 5 min): “Investigating the Function NDUFAF4 in the Context of Cholestasis”.

16:00 Much-needed coffee break

16:30 Sergio Encarnación-Guevara(20 min + 10 mins): “Chromosome 19: Progress in the characterization of proteins without assigned function.”

17:00 Heeyoun Hwang (20 min + 10 mins): “uPE1 Study with Cholangiocarcinoma and PDAC Proteome Data”

17:30 Rob Moritz (20 min + 10 mins): Collective Thoughts on the C-HPP Mission and Direction

18:00 Session Close

Retire to hotels to freshen up and then meet for aperos and dinner at a destination to be announced by Madrid Natives (Fernando).

Friday, April 26:

Session Three: Meeting the Challenge (Chairs Cecilia Lindskog + Sergio Encarnación-Guevara)

9:00 Cecilia Lindskog (Incoming Chair HPP): (20 min + 10 mins) “Solve the Protein Puzzle – The Grand Challenge to Understand the Different Pieces of the Human Proteome”

9:30 Min-Sik Kim (new Chr 13 Head, Korea): (20 min + 10 mins) “Breast Cancer Proteome and Chromosome 13”

10:00 Chris Overall (Chair C-HPP): (20 min + 10 mins) “Physiological vs. Pathological Functions of Proteins in the Grand Challenge”

10:30 Coffee break

11:00 Frank Schmidt (new Head, Chr 21, Qatar Team): (20 min + 10 mins) “How can Olink Contribute to the HPP project?”

11:30 – 12:30 Open Discussion on technologies, approaches, and bioinformatics to meet the Grand Challenge.

12:30 Meeting Close

Campus Restaurant fine dining and departure.

REGISTER HERE

HPP Papers of Note in the Journal of Proteome Research

Wed, 31 Jan 2024 16:47:04 GMT

The hallmark update paper each year is the HPP Metrics publication, is now online, lead by Dr Gil Omenn and the leaders of neXTprot, the Peptide Atlas, the HPP, C-HPP and B/D-HPP:

“The 2023 Report on the Human Proteome from the HUPO Proteome Project”, by Gilbert S. Omenn,* Lydie Lane, Christopher M. Overall, Cecilia Lindskog, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch.

ABSTRACT: Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1−4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

HUPO ECR Welcomes New Member

Tue, 30 Jan 2024 13:54:08 GMT

The HUPO Early Career Researcher (ECR) Committee is delighted to welcome Pathmanaban Ramasamy. Keep reading to know more about him!

Pathmanaban Ramasamy (Paddy) is a junior post-doc in the CompOmics group at Ghent University in Belgium. During his joint Ph.D. program between Ghent University and Vrije Universiteit Brussel, he leveraged his expertise in structural bioinformatics and proteomics informatics to unravel the role of local amino acid interactions in protein folding, fold stability, and the location of post-translational modifications (PTMs). He endeavors to unravel the "where, how, and why" of protein PTMs through a comprehensive large-scale investigation that spans these modifications within sequence, structure, and biophysical contexts.

He has been extremely active in bringing the MS proteomics and structure communities together at the European scale, investing heavily in an ELIXIR Europe-funded cross-over study between the three key communities: the 3D-BioInfo (protein structure), Intrinsically Disordered Proteins, and MS Proteomics communities. Paddy is enthusiastic about becoming a member of the HUPO-ECR and looks forward to actively contributing to the support of young proteomics researchers through his involvement with HUPO-ECR and YPIC.

Interview with 2023 HUPO ECR Manuscript Competition Finalist: Dr. Hong Wang

Tue, 30 Jan 2024 13:28:13 GMT

Prof. Hong Wang
Institute Of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, China

What is your current position and affiliation?

I am presently employed as a Principal Investigator (tenure-track Assistant Professor) at the National Key Laboratory of Blood Science, within the Institute of Hematology & Blood Diseases Hospital at the Chinese Academy of Medical Sciences & Peking Union Medical College. Concurrently, I hold the positions of Director at the Center for Advanced Technologies and Founding Director of the Mass Spectrometry Center at Haihe Laboratory of Cell Ecosystem.
How would you like your work to contribute to the field of proteomics?

In my current role at the foremost blood diseases research hospital in China and the innovative Haihe Laboratory of Cell Ecosystem, I aspire to make significant contributions to the field of proteomics. By integrating mass spectrometry-based omics with other advanced technologies, I aim to collaborate closely with clinicians to address complex clinical questions. My goal is to propel these technologies towards translational medicine, facilitating the translation of precision biomarkers and therapeutic targets into practical clinical applications. This approach seeks to bridge the gap between cutting-edge research and real-world patient care.
What have you found in the HUPO community/congress?

HUPO serves as my academic home, and participating in the HUPO congress feels akin to a holiday homecoming to reunite with family and friends. Each congress is a source of continual inspiration, fostering valuable collaborations, and exposing me to new technologies that I eagerly incorporate into my work. The sense of community and shared knowledge at HUPO events consistently propels my research forward and enriches my professional journey.
How was your experience/what did it mean to present your work at HUPO?

Presenting my work at HUPO was an enriching experience, marked by valuable and insightful feedback. The positive reception and recognition of my multidisciplinary efforts within my field provided a significant boost of confidence. This affirmation encourages me to advance further in exploring the novel concept of the blood ecosystem that we introduced, reinforcing my commitment to pioneering work at the intersection of diverse disciplines.

HUPO Proteomics Standards Initiative (PSI) Meeting 2024

Tue, 23 Jan 2024 18:56:23 GMT

The PSI meeting 2024 will take place from March 18-20th 2024 at the Kyoto University, Japan.

View event details here.

The meeting is sponsored by: JPOST (JST-NBDC) and JPDM (JSPS).

Organizers: Yasushi Ishihama & Shujiro Okuda.

Are you interested in defining the formats and standards that describe the next generation of mass spectrometry data?

Then join us at the next HUPO-Proteomics Standards Initiative (HUPO-PSI) Spring Workshop in the beautiful city of Kyoto, to work on to work on developing and updating new and existing standards, such as mzML, mzIdentML, mzSpecLib, mzPAF, mzQC, and the Universal Spectrum Identifier (USI), in the light of new methodologies and technologies.

The workshop is free to participants, and very hands-on so come prepared to actively engage with this community and present your ideas and use cases. The work of the HUPO-PSI has led to a dramatic increase in the availability of proteomics data in the public domain thanks largely to the wide adoption of open data practices in the field and we look to continue that trend as new methodologies are developed.

Thanks to our sponsors (HUPO, JPOST (JST-NBDC) and JPDM (JSPS)) we are able to offer a number of generous travel/accommodation grants - please apply for consideration to receive one of these when you register for the meeting.

Please note that if your interests lie in the field on protein/molecular interactions, this workgroup will meet virtually this year. Register as normal via the link given above and we will finalise timings subject to the geographic location of participants.

Program: The provisional agenda will be posted soon.

Registration: Registration for attending the meeting is now open.

HUPOST January 2024

Wed, 10 Jan 2024 16:45:22 GMT

The January HUPOST is now available.....check out the latest HUPO 2024 news, ETC Webinars, ECR Manuscript Competition, upcoming events & much more...

HUPO ECR Welcomes New Members!

Fri, 05 Jan 2024 13:44:03 GMT

The HUPO Early Career Researcher (ECR) Initiative is delighted to welcome Nick Riley and Mahshid Moballegh Nasery.

Nick Riley is an assistant professor of chemistry at the University of Washington. With a background in mass spectrometry instrumentation, proteomics, and glycobiology from his graduatework with Prof. Josh Coon at University of Wisconsin-Madison and his postdoctoral work with Prof. Carolyn Bertozzi at Stanford University, he now leads a research program focused on innovative bioanalytical and chemical biology technologies to investigate essential principles of glycocode regulation and dysregulation. Nick has been involved with HUPO and US HUPO for a number of years and is excited to join the HUPO ECR committee to support the vibrant and supportive communities that help early career scientists build their scientific careers in proteomics research.

Mahshid Moballegh Nasery pursued a diverse academic journey, beginning with a Bachelor's in Chemistry and delving closer into biology with a Master's in Medical Toxicology, where her focus on cancer led to publications in articles and a chapter book. Her passion for proteomics started to grow as she attended her proteomics course and attended an ECR day meeting! Currently engaged in research at the University of Debrecen, under the supervision of Dr. Eva Csosz. Her recent membership in YPIC (Young Proteomics Investigators Club) reflects her eagerness to expand her network and engage actively with fellow proteomics scientists. She aims to deepen her involvement in various activities, leveraging her multi-disciplinary background, to contribute meaningfully to the scientific community. Driven by a thirst for knowledge and a desire to make impactful contributions, Mahshid is passionate about exploring within the vibrant realm of proteomics and biochemistry.

Interview with 2023 HUPO ECR Manuscript Competition Winner: Johannes Bruno Müller-Reif

Fri, 05 Jan 2024 13:27:56 GMT

Dr. Johannes Bruno Müller-Reif

(Max Planck Institute of

Biochemistry, Germany) presented his work Immobility-associated Thromboprotection is Conserved across Mammalian Species from Bear to Human in a plenary session at HUPO 2023 in Busan, South Korea

Dr. Müller-Reif’s research is multifaceted. A cornerstone of his work involves applying mass spectrometry-based proteomics to large patient cohorts to enhance biomarker discovery. In this capacity, he co-leads the MOMI cohort’s plasma proteomics efforts to address adverse pregnancy outcomes, supported by the Bill and Melinda Gates Foundation. He also focuses on the utilization of proteomics for investigating rare pediatric diseases. Furthermore, Dr. Müller-Reif pioneers the use of proteomics in specialized applications such as platelet biology and studying organisms inaccessible through conventional methods. This innovative approach not only exemplifies the practical versatility of proteomics but also ties back to his doctoral research on the proteome landscape of the kingdoms of life.

Interview with Dr. Johannes Bruno Müller-Reif

What is your current position and affiliation?
I am a project group leader (a position somewhat between postdoc and group leader) at the Max Planck Institute of Biochemistry within the group of Matthias Mann.

How would you like your work to contribute to the field of proteomics?
I currently focus on clinical mass spectrometry-based proteomics and nearly any project I am working on involves patient samples or is a direct collaboration with clinicians. I would like to continue employing this powerful method to uncover biological mechanisms and better understand diseases, which ultimately will benefit patients with better treatments. In the best case scenario, this leads for example to the discovery of novel biomarkers or therapeutic targets, but also a better functional understanding without the identification of distinct single biomarkers is a step in the right direction. Biomarker discovery is often done with large patient cohorts and I hope to contribute to the field by enabling such studies from a technical perspective and providing the community with unique datasets. In parallel to this work, I would like to transform proteomics from a method for biomarker discovery by retrospective analysis to a tool for pro- and diagnostics in the future.

What have you found in the HUPO community/congress?
I had the chance to attend the HUPO world congresses two times so far. I found it to be a perfect intersection of different interest groups forming a thriving community between biological expertise and technical solutions.

How was your experience/what did it mean to present your work at HUPO?
Having been invited to the ECR manuscript competition to HUPO in Busan to present my work meant a lot to me. Sharing the excitement about new findings is definitely a driver of motivation for me to work as a scientist and being given the opportunity to do so in such a venue has been a major pleasure. I received a plethora of positive feedback from this wonderful community, which is truly motivating.

ETC Webinar Series: Reverse Phase Protein Array (RPPA) Applications: Molecular Profiling and Predicting Response to Targeted Therapies

Fri, 05 Jan 2024 00:38:32 GMT

DATE: Wednesday, March 20, 2024
TIME: 2pm PST / 5pm EST / 10pm CET
LOCATION: Zoom (link to follow upon registration)
SPEAKER: Rosa Isela Gallagher, PhD

REGISTER HERE

WEBINAR DESCRIPTION:

RPPA is a high-throughput protein array technology that simultaneously measures hundreds or thousands of samples on glass slides with high precision and reliability, using specific antibodies. RPPA and mass spectrometry-based protein profiling are complementary technologies for protein profiling. In attending this webinar, attendees will learn about RPPA's high-throughput capabilities and laser-captured microdissection technology. They will understand how these technologies precisely measure protein expression, modifications, and phosphorylation in tumor cells.

WHAT ATTENDEES WILL LEARN:

RPPA Technology Overview: Understand the high-throughput nature of RPPA for simultaneous analysis of numerous samples with minimal amounts. And explore how RPPA measures protein levels and modifications, offering a detailed molecular profile of tumor cells. Clinical Applications: Learn how RPPA and LCM aid in accurate diagnosis and prognosis, particularly in cancer, influencing clinical decision-making. Understand RPPA's role in predicting responses to targeted therapies, shaping the future of personalized medicine.

CLINICAL APPLICATIONS:

Learn how RPPA and LCM aid in accurate diagnosis and prognosis, particularly in cancer, influencing clinical decision-making. Understand RPPA's role in predicting responses to targeted therapies, shaping the future of personalized medicine.

SPEAKER BIO:

Dr. Rosa Isela Gallagher obtained her Ph.D. in Cell and Molecular Biology from GMU in 2019. She has accumulated more than 15 years of expertise in Reverse Phase Protein Array (RPPA) and Laser Capture Microdissection (LCM) technologies and is currently a Senior Research Scientist in the Center for Applied Proteomics and Molecular Medicine, led by Drs. Lance Liotta and Emanuel Petricoin III, the inventors of both technologies. RPPA is a high-throughput, antibody-based protein array technology capable of conducting assays on small amount of materials on thousands of samples simultaneously. This platform measures protein expression levels and modifications, including phosphorylation. Dr. Gallagher’s current research focuses on the molecular profiling of tumor cells utilizing LCM and RPPA to investigate unique signaling pathway profiles and new disease mechanisms to guide diagnosis, prognosis, and targeted therapeutics.

REGISTER HERE

HUPOST December 2023

Sat, 09 Dec 2023 02:23:11 GMT

The December HUPOST is now available.....check out the ETC webinars, HPP Chair & Co-chair nominations, C-HPP updates, upcoming events & a farewell message from HUPOST editor Ben Garcia...

ETC Webinar Series: Past, Actual, and Future Directions of Trapped Ion Mobility Time of Flight Mass Spectrometry (TIMS-TOF-MS)

Sat, 09 Dec 2023 01:02:45 GMT

DATE: Wednesday, February 21, 2024
TIME: 7am PST / 10am EST / 4pm CET
LOCATION: Zoom (link to follow upon registration)
SPEAKER: Oliver Raether

REGISTER HERE

WEBINAR DESCRIPTION:

Trapped ion mobility spectrometry (TIMS) is a powerful analytical technique that separates and characterizes gas-phase ions based on their mobility in a buffer gas. TIMS has been widely applied in various fields, such as proteomics, metabolomics, lipidomics, and pharmaceutical research. It offers sensitivity, speed, and resolution for complex and challenging samples.

LEARNING OBJECTIVES:

In the first part of this webinar, you will learn about the history of the TIMS research and development, including the chronological launch of the different timsTOF instruments and SW capabilities by Bruker. You’ll learn about the differences and similarities of the timsTOF instruments, the possible upgrade paths and software options.

In the webinar, you will also learn about the different data-independent acquisition (DIA) mass spectrometry methods currently used in proteomics and how new approaches benefit from the additional ion mobility dimension and new acquisition modes.

Finally, in the third part of this webinar, you will learn about some of the future approaches that are currently under development for the TIMS technique, such as TIMS gas phase fractionation and filtering. This is a novel setup that uses two or three TIMS analyzers in a row to separate and isolate different regions of the m/z vs 1/K0 space. This can increase the selectivity and sensitivity of the TIMS technique, and improve applications and workflows especially for heterogeneous proteomics samples. You will see how these methods work, and what are the advantages and challenges of implementing it.

SPEAKER BIO:

Oliver Raether is Research and Development Manager at Bruker Daltonics in Bremen. He received his M.Sc. in engineering from the Hamburg University of Technology (1995). Over the past nearly three decades he and his colleagues have developed orthogonal time of flight mass spectrometers including since 2010 the timsTOF product line. He has produced 14 peer reviewed journal articles and is inventor/co-inventor of 71 patents in the field of mass spectrometry and, more recently, ion mobility spectrometry (h-index 13). His awards include the HUPO Science and Technology Award for contributions on Trapped Ion Mobility Mass Spectrometry Instrumentation (2020).

REGISTER HERE

ETC Webinar Series: Why Size Matters: Revolutionizing Protein and Peptide Detection with Ion Mobility

Sat, 09 Dec 2023 00:56:30 GMT

DATE: Wednesday, January 24, 2024
TIME: 6am PST / 9am EST / 3pm CET
LOCATION: Zoom (link to follow upon registration)
SPEAKER: Daniel DeBord, PhD

WEBINAR DESCRIPTION:

Protein identification is of fundamental importance in many areas of proteomics. Its applications include determining the presence or absence of an expected protein in a sample of interest, identifying an unknown protein present in a biological sample, and identifying a protein responsible for biochemical activity in an isolated protein fraction. In some cases, mass spectrometry or affinity-based methods may be suitable options, but these methods can face substantial challenges. Scientists need the ability to identify and measure peptide modifications, structures, and impurities more definitively and faster. Driven by structures for lossless ion manipulation (SLIM) technology, the MOBIE® instrument’s high-resolution ion mobility mass spectrometry platform separates and identifies the most challenging molecules with unprecedented resolution without compromising speed. By combining the MOBIE® platform’s high-resolution ion mobility mass spectrometry (HRIM-MS) data with liquid chromatography, more accurate separation and identification of impurities and posttranslational modifications (PTMs) can be achieved, reducing run times and costs.

LEARNING OBJECTIVES:

Attendees will learn Attendees will learn about (1) separation science, including SLIM (structures for lossless ion manipulation) and high-resolution ion mobility (HRIM); (2) the trade-off between speed, resolution, and reproducibility; and (3) accuracy for targeted lipidomics, peptide characterization, glycan analysis, PFAS, and many other workflows.
Why Attend? AAttendees will uncover insights into how to incorporate HRIM into traditional analytical workflows and where the technology is used to answer clinical questions.

SPEAKER BIO:

Daniel currently serves as the Vice President of R&D for MOBILion Systems, Inc. In this role, he leverages his 15 years of experience developing novel analytical instrumentation to address challenges across a range of application spaces. Daniel received a BS in Chemistry from Campbell University and a Doctorate in Analytical Chemistry from Texas A&M University. Prior to starting work with MOBILion, he served as the Chemistry Manager and lead developer for 1st Detect Corporation, a company that develops miniaturized mass spectrometry-based detection systems for a variety of markets. Daniel also worked as a staff Research Scientist and Associate Director of the Mass Spectrometry Facility at Florida International University and as an LC‒MS chemist for BASF. For the past 10 years, Daniel has focused on developing ion mobility technologies such as trapped ion mobility spectrometry (TIMS) and structures for lossless ion manipulation (SLIM) and exploring how these new techniques can be coupled with traditional LC‒MS instruments to access higher performance in fields such as proteomics and biopharma characterization.

REGISTER HERE

Human Proteome Project (HPP): Recruitment of The Chair and Co-chair

Fri, 17 Nov 2023 13:08:16 GMT

The Human Proteome Project (HPP) was launched in 2010 under the aegis of HUPO. The vision of HUPO is that HPP activities will collectively and ultimately lead to breakthroughs enabled by proteomics, in medicine, biotechnology and the life sciences, thereby leaving a legacy of human proteome research.

The HPP continues to make progress, addressing three major components, Chromosome-HPP (C-HPP), Biology and Disease-HPP (BD-HPP) and the HPP-Grand Challenge. It is focused on:

Cataloguing the human protein ‘parts’ list with high accuracy.
Understanding the complexity and function of the human proteome (including post-translational modifications, splice variants, proteoforms, small proteins/peptides, etc.).
Document and provide data deposition and analysis globally through portals (e.g., ProteomeXchange) and via major specific efforts (e.g., Human Protein Atlas, PeptideAtlas, neXtProt) with communal guidelines/metrics published with an annual communal reanalysis of whole human proteome’s protein existence (PE) status and making proteomics an integrated complement across the clinical, biomedical and life sciences research space.
In 2021, the HPP inaugurated the establishment of the HPP Grand Challenge project “A function for every protein”.

ROLES / RESPONSIBILITIES:

Chair

The HPP Chair leads the development and implementation of the Human Proteome activities of the C-HPP, the B/D-HPP and the HPP Grand Challenge. The term of the HPP Chair is two years and so the position becomes vacant on December 31, 2024. To ensure a smooth and consistent transition, the incoming Chair will sit on the HPP EC for one year (2024) prior to their 2-year term (2025-2026) and also be present as past Chair in 2027.

Co-chair

The HPP Co-Chair helps lead the development and implementation of the Human Proteome activities of the C-HPP, the B/D-HPP and the HPP Grand Challenge with the HPP Chair. The term of the HPP Co-Chair is two years and is staggered with appointment of the HPP Chair. The HPP Co-Chair position becomes vacant on December 31, 2023, for a 2-year term (2024-2025).

Responsibilities:

Chair the HPP Executive Committee and work with the HPP strategic advisory group to maximize the impact of HPP
Evolve and implement the strategic goals of the HPP by working with the HPP Executive Council and its membership to accelerate progress, assess the goals and performance of each component, and connect the components of the HPP
Supporting all HPP initiatives (C-HPP, B/D-HPP) and the HPP Grand Challenge
Represent the HPP on the HUPO Executive Committee monthly calls
Represent the HPP at national/international/strategic meetings, as needed
Liaison with other HUPO Committees (e.g., HUPO Marketing and HUPO Early Career Committee) and initiatives (e.g., Antibody and Single Cell) to support the development of science and education
Work with HUPO External Development Committee (HEDI) and the HUPO EC to work on strategic projects and funding with other resources for the scientific community

QUALIFICATIONS

HUPO is currently seeking scientifically strong, strategic, vibrant, enthusiastic and collegial leaders who will be suitable candidates to lead, build, advance, and represent the HPP. HUPO is keen to ensure regional and gender equity across its management structures. This position is honorary and in line with the many organizational positions within the HUPO Executive Committee.

APPLICATIONS

All candidates must be active HUPO members and scientists from the public or private sector with professional experience in the educational, research, or commercial activities related to the HPP. Applications will be accepted and a vote conducted. The successful candidate will be reviewed and approved by the HUPO Executive Committee.

To apply, please submit:

Your CV
A recent photo (in JPEG high-resolution format)
A statement of the position in which you are applying
A one-page vision statement outlining why you are a suitable candidate for the position.

SUBMISSIONS

To: office@hupo.org

Deadline: December 15, 2023

QUESTIONS

Email Charles Pineau (current HPP Chair) charles.pineau@inserm.fr

HUPOST November 2023

Thu, 02 Nov 2023 00:22:30 GMT

The November HUPOST is now available, full of HUPO news and proteomics community information and updates

Did You Miss the Mentoring Sessions at HUPO 2023? Here are some Highlights and Key Takeaways!

Mon, 30 Oct 2023 22:06:13 GMT

AI Tools in Grant Writing Applications, Research Articles, CVs, etc.

Chairs: Emily Hashimoto-Roth (University of Toronto, Canada) and Ruth Huttenhain (Stanford University, USA)

Speakers:

Dr. Laura Elo (University of Turku, Finland)
Dr. Min-Sik Kim (Daegu Gyeongbuk Institute of Science & Technology, South Korea)
Dr. Jack Washington (Molecular Omics, United Kingdom)

The session "AI tools in grant writing applications, research articles, CVs, etc." focused on the integration of new artificial intelligence (AI) technologies into various aspects of scientific document production and publication.

Attendees shared the utility of AI tools such as ChatGPT to enhance their daily work efficiency, mentioning that these tools are quite useful for brainstorming and idea generation. In particular, using ChatGPT as a writing aid was recognized as a valuable tool to overcome writer's block or "blank-page-o-phobia”. It was also discussed how AI tools can also be very useful for editing and proofreading, especially when English is not the writer’s first language. The potential use of AI by journals for proofreading to identify formatting and writing errors was also discussed, indicating the evolving role of AI in scientific publishing.

Participants also questioned mentors regarding best practices for AI tools in research. IN short it was mentioned that AI can be leveraged to polish visualization, troubleshoot software code, and even interpret results, but such tools should be used with caution. Despite the benefits of using ChatGPT prompts for writing, the need for critical review and manual editing to ensure the final written output meets scientific standards was emphasized. Ethical concerns, including the risk of data leaks when using AI tools for proofreading and the need for transparency of AI contributions was mentioned. Overall, the session shed light on the growing role of AI in proteomics research and the broader scientific publishing landscape. It offered an exploration on AI’s potential to enhance efficiency, address ethical concerns, and possibly reshape the way scientific research is published and shared in the future.

Promoting Your Science

Chairs: Daniel Garama (Hudson Institute of Medical Research, Australia) and Mathieu Lavallée-Adam (University of Ottawa, Canada)

Speakers:

Dr. Alexey Nesvizhskii (University of Michigan, USA)
Dr. Hyun Woo Park (Yonsei University, South Korea)
Dr. Stephen Pennington (University College Dublin, Ireland)
Paula Burton (Mass Dynamics, Australia)

This session explored the many aspects of promoting your science as well as how scientific outreach can help in advancing one’s career.

It was clearly highlighted during the session that one key aspect of promoting your science involves, identifying target audiences. In addition to attending specialized conferences, participants discussed alternative methods for identifying the right audience for their research. Strategies included utilizing social media, publishing in widely read journals, and engaging with interdisciplinary communities. The session touched on the topic of maintaining a professional online presence. While recognizing the value sharing elements of one’s personal life, participants advised caution about posting some personal photos online, emphasizing the usefulness of a separate professional profile to maintain a credible image.

Attendees also discussed the role of institutional support in self-promotion. Many shared how universities, institutes, and companies can provide resources, such as funding, mentorship, and networking opportunities, to aid in career advancement and science promotion. Interestingly, participants considered some of the challenges related with dealing with opposition. Speakers shared their experiences on how they find the courage and confidence to address opposition to their ideas and results. The importance of constructive feedback, resilience, and persistence was highlighted. Finally, the panelists emphasized the importance of diversity and inclusion efforts in academia and research.

Geographical Differences for Academic Job Applications

Chairs: Andreas Hober (AstraZeneca, Sweden) and Lívia Rosa-Fernandes (Macquarie University Centre for Motor Neuron Disease Research, Australia)

Speakers:

Dr. Nicki Packer (Macquarie University, Australia)
Dr. Uwe Völker (University Greifswald, Germany)
Dr. Yu-Ju Chen (Academia Sinica, Taiwan)
Dr. Birgit Schilling (Buck Institute, USA)

During this session, attendees learned about the added value of conducting research abroad. In particular the benefits of exposure to different scientific cultures and networking opportunities were highlighted. Still, it was acknowledged that working abroad is not a universal requirement for a successful career. International relocation can have profound effects on personal aspects, such as partnerships and family. For example, some participants were curious regarding the challenges faced by expecting or new parents in finding jobs. The conversation emphasized the importance of supportive and flexible work environments to accommodate family responsibilities.

Attendees discussed the current job demand in the proteomics field, recognizing its rapid growth with increasing opportunities in academia, industry, and healthcare. Tips were shared for students aspiring to secure positions, including reaching out to potential mentors and the importance of making a good impression during a job interview by attaining to a professional etiquette. For graduate students interested in finding postdoctoral positions, panelists shared how most postdocs typically find their positions, highlighting networking, collaborations, and mentor recommendations as effective strategies. The timing of grant applications for postdoctoral researchers and beyond was a significant topic. Advice emphasized starting early, cultivating strong grant-writing skills, and being strategic.

In addition, participants acknowledged diverse career paths within proteomics research outside of the traditional academic route. These paths encompassed roles in scientific communication, project management, bioinformatics, and more. Some attendees expressed their interest in transitioning to industry and panelists debated the optimal timing for transitioning from academia to industry. It was agreed that this decision should be based on individual career goals and the alignment of research interests with industry demands.

HUPOST October 2023

Thu, 12 Oct 2023 21:03:47 GMT

The October HUPOST is now available featuring HUPO 2023 Wrap Up, Congress Photos, Competition Winners, Election results and much more!

A Community Effort to Comparatively Evaluate Single-Cell Proteomics Technologies

Fri, 06 Oct 2023 13:49:18 GMT

The main goal of the new HUPO single-cell proteomics (SCP) initiative is to provide guidance and create a comparative overview of novel mass spectrometry (MS)-based low-input and single-cell technologies. After the first reports of SCP with large cells (i.e., oocytes) the field has quickly moved to ever more comprehensive analysis of single mammalian cells or even subcellular components.^1–3 A variety of workflows have since demonstrated valuable insights into cellular identities and their function, driven entirely by the proteome and their post-translational modifications.^4–6 However, deep proteome profiling of single mammalian cells or small subpopulations remains an analytical challenge for most non-specialized laboratories.

The growing interest in the SCP workflows and its application to biological questions has driven the initiation of this international SCP initiative. Our team is comprised of a diverse group of early, middle and advanced level scientists with growing expertise in diverse workflows and instrumentation. We aim to provide a comparative overview of current SCP approaches for the community to ease the implementation in more laboratories and integration to novel biological projects. Considering the ongoing trend away from bulk analysis towards resolving cellular heterogeneity, we believe that such unifying efforts will drive the understanding of complex tissue hierarchies and orchestrated spatiotemporal interactions.

To this end, our first goal is to perform a multi-laboratory study, processing the same batch of cells across different platforms and establish the first of such direct comparisons. We will leverage the knowledge of our SCP initiative members, who have pioneered various parts of the SCP workflows, including sample collection and preparation, chromatographic separation, acquisition strategies and analysis approaches.^2,3,7–9 We consider utilization of one cell batch especially important for these comparisons, as cell handling and the cell cycle heavily influence cell size and proteome composition.^5,10 Our portfolio of SCP workflows will include isobaric multiplexing (i.e. TMT) with one chemical label for multiple cells (i.e. carrier - SCoPE) to facilitate sufficient peptide signal even with less sensitive MS instrumentation.² Following tremendous improvements in instrument sensitivity and implementation of ion-mobility separation also label-free SCP workflows have been successfully demonstrated.^5,11 Those are typically paired with data independent acquisition (DIA), which massively reduces precursor stochasticity in comparison to data dependent acquisition.¹² Most standard TMT-based workflows rely on small isolation windows to reduce precursor co-isolation to relatively quantify a single precursor through their reporter ions.¹³ Scanning speeds of current instrumentation therefore restrict isobaric labeling workflows to DDA, which suffer from detrimental amounts of missing data across large sample cohorts.¹² The alternative label-free SCP approaches, however, are notoriously low in throughput as only once cell at a time is being analyzed in comparison to the isobaric labelling strategies (i.e. TMTpro = 18 samples or HyperSCP = 28).^14,15 As most applications for SCP require the analysis of hundreds or even thousands of cells, most recently a combination of non-isobaric chemical labeling with DIA allowing for relative quantification between up to three samples at the MS1 level was introduced.^16,17 This reduces missingness across a large number of samples while still increasing throughput through multiplexing.

As an alternative to chemical multiplexing, many groups aim to increase measurement throughput by optimizing chromatographic separation. Due to their low input, SCP samples do not require such extensive separation, allowing for the effective gradient length to be reduced in comparison to bulk.^5,18–22 Short gradients and most efficient inject-to-inject times has been implemented with the disposable trap columns of the Evosep One. Those are regularly used for SCP workflows, due to the combination of in-line clean up the sample and simultaneous separation of peptides, while the previous sample is still acquired on the MS.^5,23,24 SCP initiative team members also most recently demonstrated significantly reduced separation times employing non-commercial alternatives to increase chromatographic throughput.^18,21,22 Additionally, to the various acquisition and peptide separation efforts, the SCP community has proposed smart strategy to streamline sample preparation for reduced peptide losses and improved reproducibility.^{2,7,8,11,20,25–27} Our comparative analysis will therefore include both plate-based sample preparation at higher volumes (i.e. 1-3uL) and dedicated chip or slide based approaches with low nanoliter volumes within dedicated instruments such as the cellenONE and Tecan Uno.^{3,7,20,27–29}

The entire proteomics community, but especially researchers focusing on improvements in SCP, are heavily dependent on instrumentation sensitivity and throughput advances. The introduction of the Thermo Fisher Scientific Astral combining the Orbitrap and a novel asymmetric track lossless analyzer with optimized ion transfer and flight track design was readily awaited.^30–32 The combination of 200 Hz scanning speed in the Astral analyzer with the unprecedented resolution of the Orbitrap demonstrates great potential for profiling single cells.³² This now complements SCP studies regularly performed on earlier generation Orbitrap instruments, most recently linear ion trap analyzers and the highly sensitive time-of-flight instruments with trapped ion-mobility separation for operation at 100% duty cycle.^3,5,33,34 The latter has been updated this year to the Bruker Daltonics timsTOF Ultra with a more efficient ion source, allowing more ions to enter the instrument and thereby again boosting sensitivity, as well as improving dynamic range.^10,35 The combination of instrument vendors striving to improve sensitivity and throughput paired with the introduction of alternative acquisition strategies and outside the box thinking is pushing the field forward every day. Our SCP initiative therefore aims to support further development, provide a comparative overview of many techniques for multidisciplinary scientists and guide study design to make SCP more readily available for the scientific community.

Contributed by Dr. Budnik Bogdan, chair of the B/D-HPP single-cell initiative

References:

1. Lombard‐Banek, C., Moody, S.A., and Nemes, P. (2016). Single-Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16-Cell Frog (Xenopus) Embryo. Angewandte Chemie International Edition 55, 2454–2458. 10.1002/anie.201510411.

2. Budnik, B., Levy, E., Harmange, G., and Slavov, N. (2018). SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. Genome Biology 19. 10.1186/s13059-018-1547-5.

3. Zhu, Y., Clair, G., Chrisler, W.B., Shen, Y., Zhao, R., Shukla, A.K., Moore, R.J., Misra, R.S., Pryhuber, G.S., Smith, R.D., et al. (2018). Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS. Angewandte Chemie International Edition 57, 12370–12374. 10.1002/anie.201802843.

4. Specht, H., Emmott, E., Petelski, A.A., Huffman, R.G., Perlman, D.H., Serra, M., Kharchenko, P., Koller, A., and Slavov, N. (2021). Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biology 22, 50. 10.1186/s13059-021-02267-5.

5. Brunner, A.-D., Thielert, M., Vasilopoulou, C., Ammar, C., Coscia, F., Mund, A., Hoerning, O.B., Bache, N., Apalategui, A., Lubeck, M., et al. (2022). Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation. Molecular Systems Biology 18, e10798. 10.15252/msb.202110798.

6. Zhu, Y., Scheibinger, M., Ellwanger, D.C., Krey, J.F., Choi, D., Kelly, R.T., Heller, S., and Barr-Gillespie, P.G. (2019). Single-cell proteomics reveals changes in expression during hair-cell development. eLife 8, e50777. 10.7554/eLife.50777.

7. Ctortecka, C., Hartlmayr, D., Seth, A., Mendjan, S., Tourniaire, G., and Mechtler, K. (2022). An automated workflow for multiplexed single-cell proteomics sample preparation at unprecedented sensitivity. 2021.04.14.439828. 10.1101/2021.04.14.439828.

8. Schoof, E.M., Furtwängler, B., Üresin, N., Rapin, N., Savickas, S., Gentil, C., Lechman, E., Keller, U. auf dem, Dick, J.E., and Porse, B.T. (2021). Quantitative single-cell proteomics as a tool to characterize cellular hierarchies. Nat Commun 12, 3341. 10.1038/s41467-021-23667-y.

9. Végvári, Á., Rodriguez, J.E., and Zubarev, R.A. (2022). Single-Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death. Anal. Chem. 94, 9261–9269. 10.1021/acs.analchem.2c00413.

10. Evosep (2023). AN-021A - Pushing-the-boundaries-for-robust-and-high-throughput-single-cell-proteomics.pdf. https://www.evosep.com/wp-content/uploads/2022/12/AN-021A-Pushing-the-boundaries-for-robust-and-high-throughput-single-cell-proteomics.pdf.

11. Zhu, Y., Piehowski, P.D., Zhao, R., Chen, J., Shen, Y., Moore, R.J., Shukla, A.K., Petyuk, V.A., Campbell-Thompson, M., Mathews, C.E., et al. (2018). Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells. Nature Communications 9, 882. 10.1038/s41467-018-03367-w.

12. Muntel, J., Kirkpatrick, J., Bruderer, R., Huang, T., Vitek, O., Ori, A., and Reiter, L. (2019). Comparison of Protein Quantification in a Complex Background by DIA and TMT Workflows with Fixed Instrument Time. J. Proteome Res. 18, 1340–1351. 10.1021/acs.jproteome.8b00898.

13. Savitski, M.M., Mathieson, T., Zinn, N., Sweetman, G., Doce, C., Becher, I., Pachl, F., Kuster, B., and Bantscheff, M. (2013). Measuring and Managing Ratio Compression for Accurate iTRAQ/TMT Quantification. Journal of Proteome Research 12, 3586–3598. 10.1021/pr400098r.

14. Liang, Y., Truong, T., Saxton, A.J., Boekweg, H., Payne, S.H., Van Ry, P.M., and Kelly, R.T. (2023). HyperSCP: Combining Isotopic and Isobaric Labeling for Higher Throughput Single-Cell Proteomics. Anal. Chem. 95, 8020–8027. 10.1021/acs.analchem.3c00906.

15. Li, J., Cai, Z., Bomgarden, R.D., Pike, I., Kuhn, K., Rogers, J.C., Roberts, T.M., Gygi, S.P., and Paulo, J.A. (2021). TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing. J Proteome Res 20, 2964–2972. 10.1021/acs.jproteome.1c00168.

16. Derks, J., Leduc, A., Wallmann, G., Huffman, R.G., Willetts, M., Khan, S., Specht, H., Ralser, M., Demichev, V., and Slavov, N. (2022). Increasing the throughput of sensitive proteomics by plexDIA. Nat Biotechnol, 1–10. 10.1038/s41587-022-01389-w.

17. Thielert, M., Itang, E.C., Ammar, C., Rosenberger, F.A., Bludau, I., Schweizer, L., Nordmann, T.M., Skowronek, P., Wahle, M., Zeng, W.-F., et al. (2023). Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel. Molecular Systems Biology n/a, e11503. 10.15252/msb.202211503.

18. Zheng, R., Matzinger, M., Mayer, R., Valenta, A., Sun, X., and Mechtler, K. (2023). A high-sensitivity low-nanoflow LC-MS configuration for high-throughput sample-limited proteomics. 2023.04.27.538542. 10.1101/2023.04.27.538542.

19. Xiang, P., Zhu, Y., Yang, Y., Zhao, Z., Williams, S.M., Moore, R.J., Kelly, R.T., Smith, R.D., and Liu, S. (2020). Picoflow Liquid Chromatography–Mass Spectrometry for Ultrasensitive Bottom-Up Proteomics Using 2-μm-i.d. Open Tubular Columns. Anal. Chem. 92, 4711–4715. 10.1021/acs.analchem.9b05639.

20. Matzinger, M., Müller, E., Dürnberger, G., Pichler, P., and Mechtler, K. (2022). Robust and easy-to-use one pot workflow for label free single cell proteomics. 2022.10.03.510693. 10.1101/2022.10.03.510693.

21. Kreimer, S., Binek, A., Chazarin, B., Cho, J.H., Haghani, A., Hutton, A., Marbán, E., Mastali, M., Meyer, J.G., Mesquita, T., et al. (2023). High-Throughput Single-Cell Proteomic Analysis of Organ-Derived Heterogeneous Cell Populations by Nanoflow Dual-Trap Single-Column Liquid Chromatography. Anal. Chem. 95, 9145–9150. 10.1021/acs.analchem.3c00213.

22. Webber, K.G.I., Truong, T., Johnston, S.M., Zapata, S.E., Liang, Y., Davis, J.M., Buttars, A.D., Smith, F.B., Jones, H.E., Mahoney, A.C., et al. (2022). Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform. Anal. Chem. 10.1021/acs.analchem.2c00646.

23. Bache, N., Geyer, P.E., Bekker-Jensen, D.B., Hoerning, O., Falkenby, L., Treit, P.V., Doll, S., Paron, I., Müller, J.B., Meier, F., et al. (2018). A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics. Molecular & Cellular Proteomics 17, 2284–2296. 10.1074/mcp.TIR118.000853.

24. Ye, Z., Sabatier, P., Martin-Gonzalez, J., Eguchi, A., Bekker-Jensen, D.B., Bache, N., and Olsen, J.V. (2023). One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes. 2023.08.10.552756. 10.1101/2023.08.10.552756.

25. Johnson, K.R., Gao, Y., Greguš, M., and Ivanov, A.R. (2022). On-capillary Cell Lysis Enables Top-down Proteomic Analysis of Single Mammalian Cells by CE-MS/MS. Anal. Chem. 10.1021/acs.analchem.2c03045.

26. Johnston, S.M., Webber, K.G.I., Xie, X., Truong, T., Nydegger, A., Lin, H.-J.L., Nwosu, A., Zhu, Y., and Kelly, R.T. (2023). Rapid, One-Step Sample Processing for Label-Free Single-Cell Proteomics. J. Am. Soc. Mass Spectrom. 34, 1701–1707. 10.1021/jasms.3c00159.

27. Sanchez-Avila, X., Truong, T., Xie, X., Webber, K.G.I., Johnston, S.M., Lin, H.-J.L., Axtell, N.B., Puig-Sanvicens, V., and Kelly, R.T. (2023). Easy and Accessible Workflow for Label-Free Single-Cell Proteomics. J. Am. Soc. Mass Spectrom. 10.1021/jasms.3c00240.

28. Leduc, A., Huffman, R.G., Cantlon, J., Khan, S., and Slavov, N. (2022). Exploring functional protein covariation across single cells using nPOP. Genome Biology 23, 261. 10.1186/s13059-022-02817-5.

29. Dou, M., Clair, G., Tsai, C.-F., Xu, K., Chrisler, W.B., Sontag, R.L., Zhao, R., Moore, R.J., Liu, T., Pasa-Tolic, L., et al. (2019). High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform. Anal. Chem. 91, 13119–13127. 10.1021/acs.analchem.9b03349.

30. Stewart, H., Grinfeld, D., Giannakopulos, A., Petzoldt, J., Shanley, T., Garland, M., Denisov, E., Peterson, A., Damoc, E., Zeller, M., et al. (2023). Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis. 2023.06.02.543408. 10.1101/2023.06.02.543408.

31. Heil, L.R., Damoc, E., Arrey, T.N., Pashkova, A., Denisov, E., Petzoldt, J., Peterson, A., Hsu, C., Searle, B.C., Shulman, N., et al. (2023). Evaluating the performance of the Astral mass analyzer for quantitative proteomics using data independent acquisition. 2023.06.03.543570. 10.1101/2023.06.03.543570.

32. Petrosius, V., Aragon-Fernandez, P., Arrey, T.N., Üresin, N., Furtwängler, B., Stewart, H., Denisov, E., Petzoldt, J., Peterson, A.C., Hock, C., et al. (2023). Evaluating the capabilities of the Astral mass analyzer for single-cell proteomics. 2023.06.06.543943. 10.1101/2023.06.06.543943.

33. Phlairaharn, T., Ye, Z., Krismer, E., Pedersen, A.-K., Pietzner, M., Olsen, J.V., Schoof, E.M., and Searle, B.C. (2023). Optimizing Linear Ion-Trap Data-Independent Acquisition toward Single-Cell Proteomics. Anal. Chem. 10.1021/acs.analchem.3c00842.

34. Phlairaharn, T., Grégoire, S., Woltereck, L.R., Petrosius, V., Furtwängler, B., Searle, B.C., and Schoof, E.M. (2022). High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps. J. Proteome Res. 21, 2815–2826. 10.1021/acs.jproteome.2c00376.

35. Bruker Daltonik (2023). 1901442-timstof-ultra-ebook-rev2.pdf. https://www.bruker.com/en/products-and-solutions/mass-spectrometry/timstof.html.

HUPOST September 2023

Tue, 05 Sep 2023 20:24:20 GMT

The September HUPOST is now available featuring important congress information, 2023 HUPO Awardees, ECR activities and competition finalists and much more!

HUPO ECR Panel Discussion

Thu, 31 Aug 2023 23:27:34 GMT

Thank you to all who joined and participated in the HUPO ECR Panel Discussion on Translating Science from Benchtop to Biotech on August 9, 2023.

This panel is part of a seminar series organized by the HUPO Early Career Researcher Committee and The Young Proteomics Investigators Club (YPIC). These panels offer a space to foster professional development by engaging with the community. This time, two delightful panelists provided their time and expertise: Ruedi Aebersold (Co-founder of Biognosys) and Jarrod Sandow (Director and Senior Scientist at IonOpticks).

They commented on important considerations about scientific entrepreneurship such as intellectual property. Attendees learned about the resources often available within institutes or at incubators to refine a business plan . All in all this panel session highlighted the interesting opportunities of commercializing science, which can take the shape of a product, a service or developing proteomics technology. Thank you to our panelists and everyone that participated and made this such a great event.

Stay tuned for upcoming panel sessions!

HUPOST August 2023

Thu, 03 Aug 2023 02:09:03 GMT

The August HUPOST is now available featuring important congress information, next ECR webinar, ECR competition finalists, HUPO member notices, C-HPP workshop and more!

9th Annual Edition of HUPO ECR Manuscript Competition - See the Finalists

Mon, 31 Jul 2023 16:07:46 GMT

The HUPO ECR Committee is delighted to showcase the finalists of the 9th annual edition of the Manuscript Competition - take a look at their short bios below:

Dr. Johannes Bruno Müller-Reif
Max Planck Institute Of Biochemistry, Germany

Dr. Johannes Bruno Müller-Reif is a project leader and head of the Pediatric Proteomics Group at the Max Planck Institute of Biochemistry (MPIB). During his doctorate with Prof. Matthias Mann he focused on extending proteomics across the tree of life. Following his PhD, he joined the proteomics start-up OmicEra, where he significantly contributed to high-throughput proteomics methods for biomarker discovery and clinical research. Concurrently, Dr. Müller-Reif maintained a relationship with MPIB as a guest scientist, and his growing expertise led him to establish a research group with focus on the intersection of mass spectrometry-based proteomics and pediatrics. Dr. Müller-Reif’s research is multifaceted. A cornerstone of his work involves applying mass spectrometry-based proteomics to large patient cohorts to enhance biomarker discovery. In this capacity, he co-leads the MOMI cohort’s plasma proteomics efforts to address adverse pregnancy outcomes, supported by the Bill and Melinda Gates Foundation. He also focuses on the utilization of proteomics for investigating rare pediatric diseases. Furthermore, Dr. Müller-Reif pioneers the use of proteomics in specialized applications such as platelet biology and studying organisms inaccessible through conventional methods. This innovative approach not only exemplifies the practical versatility of proteomics but also ties back to his doctoral research on the proteome landscape of the kingdoms of life.

Dr. Pavel Sinitcyn
Morgridge Institute For Research, United States

Pavel Sinitcyn is a distinguished Morgridge Interdisciplinary Postdoctoral Fellow at UW-Madison, conducting cutting edge research in the Joshua Coon lab. With a strong background in developing software solutions for proteomics data processing, Pavel has played a pivotal role in developing tools such as MaxQuant, MaxDIA, Perseus, and Deep Proteomic Sequencing Method.

Prof. Hong Wang
Institute Of Hematology & Blood Diseases Hospital, Chinese Academy Of Medical Sciences & Peking Union Medical College, China

Hong Wang got his Ph.D degree in 2017 at the University of Tennessee Health Science Center/St Jude Children’s Hospital in USA. After a continuous postdoc training and senior scientist experience at St. Jude, he joined the institute of Hematology and Blood diseases hospital, Chinese Academy of Medical Sciences & Peking Union Medical College in 2021. He is now a professor of the National Key Laboratory of Blood Science and Founding Director of the Center for Advanced Technologies.

Dr. Wang has developed multiple cutting-edge Mass Spectrometry-based proteomics technologies enabling ultradeep whole proteomic profiling with sub-microgram materials. He also developed advanced bioinformatics pipelines for multi-omics integration. He has published several high impact research articles on prestigious journals as corresponding/first authors in the last five years, e.g. Immunity, Cancer Cell, Nature Communications, PNAS, Genome Biology and Molecular Neurodegeneration. His research interests including: 1, to develop high-throughput single-cell and single-cell type proteomics technologies; 2, to use advanced multi-omics integrative strategies to dissect the blood ecosystems in systematic diseases.

Webinar: Translating Science from Benchtop to Biotech

Tue, 25 Jul 2023 18:23:00 GMT

HUPO Early Career Researcher (ECR) Online Panel Webinar

DATE: Wednesday, August 9, 2023
TIME: 9 am CEST (Central European Summer Time)
LOCATION: Zoom
SPEAKERS: Reudi Abersold (Co-founder of Biognosys) and Jarrod Sandow (Director and Senior Scientist at IonOpticks)

Want to learn about turning science into a business? Join us for the coming online panel discussion taking place on August 9 at 9 am CEST. This panel is part of a seminar series organized by the HUPO Early Career Researcher Committee and The Young Proteomics Investigators Club (YPIC). These seminars offer a space to foster professional development by engaging with the community. During this one-hour panel, we will hear on thoughts and views from experienced researchers on their involvement and trajectory in the establishment of successful biotechs!

REGISTER HERE

B/D-HPP Webinar on Aging and Disease

Fri, 07 Jul 2023 00:35:27 GMT

DATE: Thursday, July 20, 2023
TIME: 11 am - 1330 pm EDT
LOCATION: Zoom

Exciting B/D-HPP webinar on aging and disease coming up. Join us and listen to diverse topics in aging and disease proteomics including cancer, Alzheimer’s disease, geroscience, and others.

PLEASE NOTE: All times listed below are Eastern Daylight Time (EDT).

1100 am EDT - ROGER REDDELL - Progress Towards Utilisation of Tissue Proteomics in the Cancer Clinic

1130 am EDT - RENA ROBINSON - High-throughput Proteomics Applications in Aging & Alzheimer’s Disease

1200 pm EDT - MAGGIE LAM - Post-transcriptional Regulation of Aging and Diseases

1230 pm EDT - BIRGIT SCHILLING - TBA

1300 pm EDT - NATHAN BASISTY - Leveraging Proteomics for Translational Geroscience

1330 pm EDT - Closing Remarks

REGISTER HERE

HUPOST July 2023

Tue, 04 Jul 2023 23:57:11 GMT

The July HUPOST is now available. Lots of great info including the HUPO Council Slate of Candidates, 2023 HUPO Awardees, congress updates, ECR and ETC activities....and much more!

Congratulations to the Finalists of the Manuscript Competition

Thu, 29 Jun 2023 23:26:31 GMT

The manuscript competition is a unique opportunity for early career researchers to gain visibility in the proteomics community for their outstanding work. It serves as a platform to highlight the important contributions that postdoctoral fellows, young clinicians and junior faculty members make to the proteomics field.

Three finalists have been selected to present their publications in a dedicated plenary session at HUPO 2023 (in Busan), where an expert committee will evaluate the oral presentations to determine the “Proteomics Highlight of the Year”.

Congratulations to:

Hong Wang, Institute of Hematology, Chinese Academy of Medical Sciences, Tianjin, China
Pavel Sinitcyn, Morgridge Institute for Research, Madison, Wisconsin
Johannes Mueller, Max Planck Institute of Biochemistry, Munich, Germany

The selection of exceptional manuscripts was a challenging task amongst many impressive submissions. The ECR would like to thank the careful evaluation and dedication from the judges: Wei Wu, Tiannan Guo, Jochen Schwenk, Ho Jeong Kwon, Concha Gil, Jennifer Geddes-McAlister, Yu-Ju Chen, Christian Moritz, Benjamin Garcia, Peter Hoffmann, Tadashi Kondo, Teck Yew Low, Fabio Nogueira, Stephen Pennington, Chantragan Phiphobmongkol, Anthony Purcell, Paola Roncada, Luis Manuel Teran, Olga Vitek, Juan Antonio Vizcaino, Marc Wilkins, Bernd Wollscheid, Shamshad Zarina and Qian Zhao! Thank you!

REPORT on 5th ETC Auditorium with Dr. Juan Antonio Vizcaino

Thu, 29 Jun 2023 17:57:07 GMT

Open data practices in proteomics: the why, the how and the what for?

The goal of the ETC Auditorium "Stylish Academic Writing" professional development webinar series is to help students and trainees improve their scientific writing skills. The 5th webinar featured Dr. Juan Antonio Vizcaino, Proteomics Team Leader at the European Bioinformatics Institute (EMBL-EBI), as the lecturer. The discussion focused on the latest trends in open data practices in proteomics. Dr. Deepti Jaiswal Kundu, a Scientific Curator at the PRIDE database (EMBL-EBI) served as the host and Dr. Tiannan Guo, a Tenured Associate Professor at Westlake University, participated as a panelist.

This webinar focused on the advantages of open data sharing in proteomics and its potential to drive research, collaboration, and innovation. Dr. Vizcaino highlighted the importance of data repositories, such as PRIDE, MassIVE, JPOST, iProX, and Panorama, in facilitating open data sharing. The webinar emphasized the FAIR data principles (Findable, Accessible, Interoperable, and Re-usable) and encouraged researchers to contribute their proteomics data and promote collaboration within the scientific community. Inspiring examples of data re-use were showcased, along with the bottlenecks associated with utilizing public proteomics data, such as data complexity and lack of metadata annotation. The webinar stressed the significance of proper metadata documentation and introduced the Sample Description and Result Format (SDRF) file format to improve metadata annotation and enable meaningful re-use of proteomics data. Lastly, the challenges of data privacy, intellectual property rights, data standardization, and data curation were addressed, with strategies and recommendations provided to promote responsible and effective sharing of proteomics data.

Dr. Vizcaino also addressed some live questions (Q & A):

1. Q: How do you envision the future of the data repositories, knowing that data sets are now containing more and more samples, like single cells or instruments producing large data?

A: It’s a continuous struggle that usually happens. We keep on innovating in terms of infrastructure in terms of keeping and dealing with large data. We take the experience /suggestions from other EBI repositories (e.g. those devoted to DNA/RNA sequencing data) about how they manage large datasets.

2. Q: The availability of sample metadata is crucial for identifying samples which are an important aspect of open data practices. A single large amount of data in PRIDE have metadata missing in them. So, what are your suggestions for the submitters in PRIDE.

A: When ProteomeXchange started on that time the emphasis was put on data provision. But now it is more and more clear the necessity of more metadata. And that’s why the SDRF annotation has been proposed which is now promoted by PRIDE to submitters.

3. Q: Many journals have dedicated data availability sections where accessions are mentioned. Have you considered using these top detect publications with PRIDE id?

A: We do that. We check the abstract of the publication and the full text (in the case of open-access journals).

4. Q: Are there any options in PRIDE to keep the RAW data private even if the article is public?

A: The policy of ProteomeXchange is as soon as publication is out, the data needs to be public. There are some exceptional cases when data is sensitive like clinical data. We do not have any mechanism yet for the controlled access data but in the future, we might have to include it.

5. Q: Some data can be re-used, do you have suggestions on what type of data has been re-used?

A: Datasets that are re-used the most are the ones that are more scientifically relevant, e.g. those published in high-profile journals. A second criterium includes those which are annotated better, where people don’t have to work on those.

A full video recording of the session including the talk and Q&A session is available on the HUPO YouTube channel website (https://www.hupo.org/Webinars-and-Virtual-Presentations).

For those with no access to YouTube, an alternative link is: https://www.bilibili.com/video/BV1Ph411c7ij/?spm_id_from=333.788.recommend_more_video.-1&vd_source=052ff6e1ca06b197e00a9a80affeda05.

HUPOST June 2023

Thu, 01 Jun 2023 20:58:03 GMT

The June HUPOST is now available. Many updates this month, including important upcoming congress deadlines, ECR updates, ETC news....and much more!

C-HPP Workshop on Next Steps for the C-HPP and neXtProt

Tue, 30 May 2023 02:34:24 GMT

The C-HPP is holding a workshop prior to the HUPO 2023 Congress in Busan, Korea at the Centum Premier Hotel in the "Chelsea and Liverpool rooms" on Sunday, 17th September, 09:30 –15:00.

Those who would like to be present are asked to register for free - the sign up sheet is here.

Please pass this onto your students and colleagues who might be attending.

Agenda

09:30 Meet and Greet coffee/tea

10:00-12:00 Session 1

Welcome, quick Chromosome Team updates:

neXtProt, human proteome numbers from the 2023-04-18 release (Lydie Lane, Eric Deutsch, Nuno Banderia),
HPP (Cecilia Lindskog)
JPR Special Issue (Chris Overall)
Other business from matters arising from the PIC.
Special presentation on “Chemoproteomics as an enabling technology for the aims of the C-HPP for PTM, MPs or CP50 research” by Ho Jeong Kwon, Director, Chemical Genomics Leader Research Initiative, Yonsei University, President-Elect, Korean Society for Biochemistry and Molecular Biology (KSBMB).

12:00 - 13:00 Lunch

13:00 Session 2: Future Aims and plans for the C-HPP/HPP and neXtProt

Discussions will include new directions for the C-HPP with an action plan for Human Proteome PTM, MPs, and CP50 (as part of the Grand Challenge) incorporating neXtProt.

15:00 Meeting closes

(15:30 HUPO Council)

The 3-Minute Thesis Competition

Mon, 29 May 2023 21:04:24 GMT

Deadline extended to June 1st

The clock is ticking, and this is your last chance to seize the spotlight and share your ground-breaking work! The 3-Minute Thesis Competition challenges you to condense your research findings into a compelling and concise presentation, delivering it in just three minutes using a single static slide.

Whether you're investigating novel biomarkers, unraveling complex protein interactions, or developing cutting-edge analytical techniques, your research deserves to be heard and celebrated. The 3-Minute Thesis Competition allows you to distill your work to its essence and effectively communicate its significance to a non-specialist audience.

Selected finalists will have the exciting opportunity to compete in the final showdown, to be held during a dedicated session at HUPO 2023 Busan (September 17-21). To participate, simply submit a lay abstract via the HUPO 2023 abstract submission portal without scientific jargon that describes your Ph.D. thesis research topic for a general, non-expert audience. Abstract text should not exceed 300 words and entrants must be enrolled in a Ph.D. program.

Submit your abstract here.

Don’t Miss your Chance to Participate in the HUPO 2023 Poster Competition!

Mon, 29 May 2023 20:55:42 GMT

Deadline extended to June 1st

Last call to participate in the HUPO 2023 Poster Competition! This is your chance to showcase your research findings, innovative methodologies, and exciting discoveries to a global audience. All graduate students (Master’s and Ph.D.), as well as postdocs, are encouraged to participate in the HUPO 2023 poster competition taking place on September 17-21, 2023 in Busan, South Korea.

This competition provides a platform for you to present your work in a visually engaging format, fostering discussions and collaborations with fellow researchers. Presenting a poster allows you to highlight the significance and impact of your research while fostering meaningful interactions with colleagues from around the world. To participate, simply indicate your interest in the competition while submitting your abstract by checking the appropriate box. A set of posters will be selected as finalists and will be evaluated during the conference by a jury. Winners in both categories (graduate students and postdocs) will each receive cash prizes.

Submit you abstract here today!

Call for Papers for the 11th HPP Special Issue of the Journal of Proteome Research

Mon, 29 May 2023 19:54:27 GMT

The Journal of Proteome Research is preparing to publish its 11th annual special issue dedicated to highlighting the progress made on the HUPO Human Proteome Project (HPP). The editorial team invites you to submit a manuscript for consideration by August 15, 2023.

For this special issue, the editorial team will consider research papers encompassing the HUPO HPP Grand Challenge, Chromosome-Centric Human Proteome Project (C-HPP) and the Biology and Disease Human Proteome Project (B/D-HPP), as well from the HPP Resource Pillars (Antibody, MS, Pathology, and Knowledgebase), and short definitive reports, submitted in the Letters format, on the discovery of a missing protein(s).

More details are available at the JPR website.

HUPO HPP Special Issues of Journal of Proteome Research

Mon, 29 May 2023 19:50:13 GMT

The 10th HUPO HPP Special Issue has been published in the April issue of the Journal of Proteome Research (https://pubs.acs.org/toc/jprobs/22/4). As a consequence of lab shut downs in the pandemic, a smaller and later Special Issue was necessary. The hallmark anchor paper of every Special Issue is the HPP Metrics paper, lead by Dr Gil Omenn and the leaders of neXTprot, the Peptide Atlas, the HPP, C-HPP and B/D-HPP: “The 2022 Report on the Human Proteome from the HUPO Human Proteome Project” by Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch (https://pubs.acs.org/doi/10.1021/acs.jproteome.2c00498)

ABSTRACT: The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, “A Function for Each Protein”.

For 2024, the format of the 11th HUPO HPP Special Issue will differ. Papers focused on the HPP, the neXt-MP50, the neXt-CP50, and the Grand Challenge will be published in regular JPR issues after acceptance during this year. In December 2023 a HUPO HPP Virtual Issue will be compiled of these HPP papers and related articles published over the year.

For reports on missing protein discovery, authors must use the 2023-04-18 release of neXtProt and the checklist for the credible identification of missing proteins (https://www.nextprot.org/news/new-release-with-updated-proteomics-data).

An example of the HPP Virtual Issue is now online HUPO Human Proteome Project Virtual Special Issue, Associate Editor, Dr Chris Overall. This collection includes papers published this past year as part of the 10th HUPO HPP Special Issue, now online, along with highly cited papers from HUPO HPP SI’s of years past.

5th ETC Auditorium - Open Data Practices in Proteomics: The Why, The How and The What For?

Tue, 16 May 2023 19:46:15 GMT

DATE: Thursday, May 25, 2023

TIME: 8:00 am EDT / 1:00 pm BST

Are you curious about the cutting-edge open data practices that are revolutionizing the field of proteomics? Join us for an exciting webinar where we will explore the benefits of making data available in the public domain and how this can be achieved. Discover how these practices can unlock new opportunities for research and innovation in the field of proteomics. We will showcase some inspiring examples of how this open data is being utilized by the scientific community and share some insights on the upcoming challenges. Don't miss this opportunity to stay ahead of the curve and learn about the latest trends in open data practices in proteomics.

LECTURER: Dr. Juan Antonio Vizcaino, Proteomics Team Leader, European Bioinformatics Institute (EMBL-EBI)

PANELISTS:

Dr. Tiannan Guo (host), Tenured Associate Professor, Westlake University
Dr. Deepti Jaiswal Kundu, Scientific Curator (PRIDE archive), EMBL-EBI

REGISTER HERE

After registering, you will receive a confirmation email containing information about joining the webinar.

HUPOST May 2023

Mon, 01 May 2023 17:41:51 GMT

The May HUPOST is now available. There's lots of updates including congress info, Single Cell webinar, ECR news, HUPO Awards and Elections....and much more!

HUPO ECR Welcomes Two New Members

Sat, 29 Apr 2023 04:00:18 GMT

The HUPO Early Career Researcher (ECR) Initiative is delighted to welcome Darien Tayba Schell and Seanantha Baros-Steyl.

Darien Tayba Schell is a Ph.D. student at the University of Cape Town, South Africa, supervised by Prof. Jonathan Blackburn. Her research aims to better understand host responses to mycobacterial phosphatases during infection using phosphoproteomic methods. She is skilled in mass spectrometry, microscopy, and R programming. During her BMedSci Hons degree, specializing in structural biology, she became intrigued by mass spectrometry in relation to proteomics. She hopes that her findings contribute to the field of Tuberculosis research and provides a framework for the development of more effective TB treatments in the future. Darien looks forward to contributing to the future growth of the ECR.

Seanantha Baros-Steyl is a Ph.D. student at the University of Cape Town, South Africa, working under the supervision of Prof. Jonathan Blackburn. Her current research focuses on identifying host-pathogen protein-protein interactions within the context of tuberculosis. She employs mass spectrometry-based proteomic and phosphoproteomic pipelines to uncover the mechanisms driving disease progression and identify potential therapeutic targets. She also has a strong interest in leveraging programming languages, particularly Python and R, to enhance mass spectrometry data analysis and visualisation. Seanantha is passionate about diseases of the developing world and strives to use her expertise to contribute to the advancement of drug discovery and development and improve the lives of people affected by these diseases. She is committed to making a positive impact within the HUPO community.

Introducing the Newly Elected Members of the HUPO-HIPP Leadership Team

Sat, 29 Apr 2023 02:07:20 GMT

We are pleased to announce the results of the 2023 HIPP election. We would like to thank Jenn Abelin, Nicola Ternette and Wei Wu for agreeing to stand for election. The newly elected members of the HUPO-HIPP leadership team are:

Chair: Nicola Ternette Co-chair: Jenn Abelin
University of Oxford Broad Institute

A word from our newly elected Chair:

Thank you all for your participation in the HUPO-HIPP elections 2023! I am very honoured to take on the position as Chair of HUPO-HIPP together with Jenn Abelin. We would like to take this opportunity to thank Michal Bassani for her excellent leadership throughout the past two years, which enabled us to present and discuss important findings in the field in three high-profile webinars and allowed us to hold the 2nd HUPO-HIPP Summer School in Oxford, UK last year.

Jenn and I will continue our efforts to facilitate discussions in the field of immunopeptidomics together with the executive committee, with its current members Michal Bassani, Pouya Faridi, Annika Nelde, Krystel Vincent, and Wei Wu. We would also like to welcome Susan Klaeger to the executive committee, as our first industry representative. We are keen to learn whether there are suggestions or nominations for additional members of our committee, and or hearing from you what would be a priority for the HUPO-HIPP team from your perspective. Do not hesitate to contact us at hupo.hipp@gmail.com.

We will get in touch soon with more information on the establishment of working groups and activities not to miss in the immunopeptidomics community.

All best wishes,

Nicola & Jenn

HUPO Single Cell Initiative Webinar

Tue, 04 Apr 2023 21:11:58 GMT

DATE: Tuesday, May 2, 2023

TIME: 8 am PDT / 10 am CDT / 11 am EDT

SPEAKERS AND PRESENTATION TOPICS:

Vadim Demichev: “Using Slice-PASEF to maximise proteomics sensitivity.”
Manuel Matzinger: “High throughput single cell proteomics using ultrashort gradients and Wide-Window Acquisition to reach unprecedented proteome coverage and quantitative accuracy.”
Ben Osborn: ”Applying single cell proteomics to answer questions in human pharmacology”
Claudia Ctortecka: “Versatile and reproducible single-cell protein profiles define cell sub-populations at high throughput”
Sarah Parker: “Single Cell Proteomic Analysis of Complex Tissue: Case study in the Aorta”

REGISTER HERE

HUPOST April 2023

Mon, 03 Apr 2023 16:40:36 GMT

The April HUPOST is now available. See Congress Updates, ECR & ETC Webinars + Much More!

4th ETC Auditorium - Writing: The Key to Funding Your Research

Thu, 30 Mar 2023 22:15:29 GMT

Join us for the 4th ETC Auditorium - Writing: The Key to Funding Your Research

DATE: Wednesday, April 12, 2023

TIME: 7 am PDT / 9 am CDT / 10 am EDT

Writing a successful grant application is hard work—regardless of your career level. Once you've convinced yourself that you have a compelling research project, you have to find a way to convince the reviewers and then the funding agency to support you. This webinar will cover fundamental essentials of a successful research proposal, including choice of grant category, PI and collaborators/co-investigators in addition to writing style, organization, and documentation. Guidance about shared instrumentation grant applications will also be presented.

SPEAKER: Dr. Susan Weintraub has been been actively engaged in biomedical mass spectrometry since 1971. She is a co-author of more than 180 scientific papers published in peer-reviewed journals in addition to six book chapters. She completed a six-year term on the Board of Directors of the American Society for Mass Spectrometry (ASMS), serving as Vice President for Programs (2010 - 2012), President (2012 - 2014) and Past President (2014 - 2016). She is currently a member of the HUPO Council and chair the HUPO Mass Spectrometry Resource Pillar. She is also an Associate Editor for the Journal of Proteome Research, with a primary assignment of computational mass spectrometry manuscripts. In 2018, she was elected a Fellow of the American Association for the Advancement of Science. Dr Weintraub's publications can be found in her PubMed Bibliography

PANELISTS:

Giuseppe Palmisano: Professor - Department of Parasitology, University of Sao Paulo, Brazil
Brian Searle: Assistant Professor - Department of Biomedical Informatics, State Ohio University Medical

REGISTER HERE

After registering, you will receive a confirmation email containing information about joining the webinar.

Summary of 3rd ETC Auditorium with Ruedi Aebersold: "Career Advancement is Dependent on Paper Writing"

Thu, 30 Mar 2023 22:12:31 GMT

The goal of the ETC Auditorium "Stylish Academic Writing" professional development webinar series is to help students and trainees improve their scientific writing skills. The 3rd event featured Ruedi Aebersold from ETH Zurich, Switzerland. Prof. Ruedi Aebersold is an emeritus Professor at ETH Zurich who is an international leader in proteomics field and mentored many scientists. Ruedi's lab has pioneered several widely-used techniques and tools that have contributed to today's proteomics research. His publications have been cited 196,000 times with an h-factor of 214, according to Google Scholar.

The talk emphasized a number of key ideas on why and how paper writing contributes to a successful scientific career as a significant factor, including:

A paper only matters if it describes progress in the field
Publishing your work in a way that supports your career goals
The reason why prestigious journals have a high IF is that they manage to include a small number of papers that have >100-1000s citations
Publications that are more cooperative generally have a higher impact, especially those describing research at the interface of disciplines
Make the text easier and clear: One paper one message
Before you start writing: define the science story and tell it to the lab and other audiences who are not scientists
Use a foolproof structure and track through the main topics e.g., the discussion should be focused on putting the new results in context and point out limitations
Developing writing skills by practicing writing and structured talks and using short clear sentences
Before you submit: anticipate what reviewers might object to and make sure every co-author agrees with the paper.
Grow a "thick skin" towards rejections: never take the rejection personally and improve and address the criticism factually.
Talk to the editors to adjust expectations for additional data and grievances with reviewers.
Avoid frequent problems: write one paper at a time- but do it.
Perfection is an elusive goal: freeze the story at the point of saturation and let reviewers define the path to perfection.
After publishment: increase the paper's visibility and impact through social media and conferences.

Ruedi also addressed some voted live questions from PollEverywhere, such as his views on ChatGPT and how that would affect scientific writing.

The session was hosted by Yansheng Liu (Yale University School of Medicine), Blandine Chazarin (Cedars-Sinai Heart Institute), and Deepti J Kundu (PRIDE and EBI).

A full video recording of the session including the figure clinic and Q&A session is available on the HUPO YouTube channel. An alternative link for those who don’t have access to YouTube can be viewed here.

ECR Manuscript Competition - Interviews with 2022 Finalists

Wed, 29 Mar 2023 20:37:39 GMT

The manuscript competition is a great opportunity for early career researchers to showcase their work. Each year three finalists are selected to present their manuscripts in a plenary session during HUPO’s world congress. We reached out to last year’s finalists and asked a few questions to learn about their experience in the competition at HUPO 2022 in Cancun, Mexico. Take a look at what they had to say.

Ling Hao’s Interview:

Dr. Ling Hao was a finalist in the 2022 HUPO ECR manuscript competition, for which she presented her work: Thiol-Cleavable Biotin for Chemical and Enzymatic Biotinylation and its Application to Mitochondrial TurboID Proteomics in a plenary session. We asked a few questions to Dr. Hao about her experience in the competition. Read what she had to say below!

What is your current position and affiliation?

I am an Assistant Professor of Chemistry in the George Washington University in Washington, DC, USA.

How would you like your work to contribute to the field of proteomics?

I hope that our research work can lead to both proteomics method advancements and a deeper understanding of molecular mechanisms of brain diseases. I also hope to support students and postdocs through classroom teaching and individual mentoring, so that they can enjoy research and pursue their dream careers in the proteomics field.

How was your experience and what did it mean to you to present your work at the HUPO World Congress?

It was a tremendous honor and encouragement to present our research during the 2022 HUPO ECR manuscript competition and also be selected as the HUPO Rising Star Award. I received a lot of valuable feedback to improve our research work. I felt much empowered to continue our research, pushing our science forward and supporting young researchers in the field.

What have you found in the HUPO community/congress?

I deeply appreciate and value both the exciting science and supportive environment in the HUPO community. My proteomics journey started when I was a graduate student in Prof. Lingjun Li's group in University of Wisconsin-Madison. Learning how cutting-edge proteomics techniques were developed to advance diverse aspects of human health (both in the Li Lab and during HUPO Congress) were eye-opening experiences. During the 2022 HUPO Congress, I learned about the exciting new pi-hub project as the proteomic navigator of the human body. I was also super impressed by how amazing and supportive the HUPO ECR group is.

Wout Bittremieux’s Interview:

Dr. Wout Bittremieux was a finalist and first prize winner in the 2022 HUPO ECR manuscript competition. He presented his work on: A learned embedding for efficient joint analysis of millions of mass spectra.

What is your current position and affiliation?

I recently started as an assistant research professor at the University of Antwerp, Belgium.

How would you like your work to contribute to the field of proteomics?

Building on recent breakthroughs in artificial intelligence that have led to disruptive advances across many scientific domains, my career is oriented towards developing powerful computational solutions to uncover novel biological and biomedical insights from proteomics data.

What have you found in the HUPO community/congress?

HUPO has an extremely vibrant and welcoming community. I was especially impressed by the various dedicated activities for early career researchers, as well as the open and friendly atmosphere throughout the entire conference.

How was your experience/what did it mean to present your work at HUPO?

The HUPO 2022 World Congress was my first time attending the HUPO meeting and I had a blast. With engaging discussions in the Bioinformatics Hub, an exciting scientific program, participating in the ECR Manuscript Competition, and even a little bit of beach time in between, HUPO 2022 was the year's highlight.

Ready to apply? Click here to learn more about how you can submit your work for the competition.

AMP®-Parkinson's Disease Progression Prediction

Wed, 29 Mar 2023 18:17:35 GMT

Use protein and peptide data measurements from Parkinson's Disease patients to predict progression of the disease.

Goal of the Competition:

The goal of this competition is to predict MDS-UPDR scores, which measure progression in patients with Parkinson's disease. The Movement Disorder Society-Sponsored Revision of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS) is a comprehensive assessment of both motor and non-motor symptoms associated with Parkinson's. You will develop a model trained on data of protein and peptide levels over time in subjects with Parkinson’s disease versus normal age-matched control subjects.

Your work could help provide important breakthrough information about which molecules change as Parkinson’s disease progresses.

Context:

Parkinson’s disease (PD) is a disabling brain disorder that affects movements, cognition, sleep, and other normal functions. Unfortunately, there is no current cure—and the disease worsens over time. It's estimated that by 2037, 1.6 million people in the U.S. will have Parkinson’s disease, at an economic cost approaching $80 billion. Research indicates that protein or peptide abnormalities play a key role in the onset and worsening of this disease. Gaining a better understanding of this—with the help of data science—could provide important clues for the development of new pharmacotherapies to slow the progression or cure Parkinson’s disease.

Current efforts have resulted in complex clinical and neurobiological data on over 10,000 subjects for broad sharing with the research community. A number of important findings have been published using this data, but clear biomarkers or cures are still lacking.

Competition host, the Accelerating Medicines Partnership® Parkinson’s Disease (AMP®PD), is a public-private partnership between government, industry, and nonprofits that is managed through the Foundation of the National Institutes of Health (FNIH). The Partnership created the AMP PD Knowledge Platform, which includes a deep molecular characterization and longitudinal clinical profiling of Parkinson’s disease patients, with the goal of identifying and validating diagnostic, prognostic, and/or disease progression biomarkers for Parkinson’s disease.

Your work could help in the search for a cure for Parkinson’s disease, which would alleviate the substantial suffering and medical care costs of patients with this disease.

Visit Kaggle.com to Join the Competition and for details on the competition's:

Description
Evaluation
Timeline
Prizes
Code Requirements

B/D-HPP: FragPipe Enables One-Stop Data Analysis for Bottom-Up Proteomics

Wed, 29 Mar 2023 16:58:25 GMT

Written by: Fengchao Yu and Daniel A. Polasky, University of Michigan, USA

Mass spectrometry-based proteomics is a widely used technique to study peptides and proteins quantitatively. This approach has several advantages over other techniques, such as high throughput and sensitivity. However, the data analysis process is challenging, due to the complexity of tandem MS data and wide variety of experiments and workflows under the umbrella of proteomics. To overcome these challenges, various tools have been developed to process mass spectrometry data. Unfortunately, these tools typically focus on specific aspects of data analysis, such as peptide identification, protein identification, or quantification, requiring researchers to learn and “link” multiple tools to complete the analysis. Such a process can be time-consuming and often requires specialized knowledge, limiting the growth of proteomics in the broader research community. Complete, user-friendly software suites for proteomics have been developed commercially, but are expensive and may have limited capability to be adapted to new methods and applications. Aiming to strike a balance in this space, FragPipe is an open-source and freely available graphical user interface (GUI)-based software suite that provides a one-stop solution to streamline the processing of proteomics data from raw data to result tables.

FragPipe combines state-of-the-art tools in many areas of proteome informatics to process mass spectrometry data from identification to quantification. It leverages MSFragger1-3, a fast database search engine, to perform database searching. It also couples MSBooster and Percolator4 to re-score peptide-spectrum matches (PSMs) using deep-learning predicted features, and Philosopher5 for false discovery rate (FDR) estimation. In addition, FragPipe contains several results processing tools, such as PTM-Shepherd6, which is used to discover post-translational modifications and characterize their fragmentation. IonQuant7 is used for label-free and isotopic-labeling quantifications, while TMT-Integrator is used for isobaric-labeling quantification. Finally, recent additions of a spectrum viewer, FP-PDV8, for summarizing results and viewing annotated spectra, and FragPipe-Analyst for downstream results processing and comparison of different experimental conditions have expanded FragPipe into a complete pipeline for proteomics data.

Most of the individual tools within FragPipe are being continuously developed and improved, offering cutting-edge capabilities with the convenience of a stable and user-friendly pipeline. For example, FragPipe hosts a set of advanced tools for glycoproteomics data analysis, including MSFragger Glyco search9, glycan composition assignment and FDR in PTM-Shepherd10, and O-Pair for O-glycan localization11. Analyzing glycoproteomics data is a challenging process, requiring characterization of both peptide and glycan components from glycopeptide mass spectra. MSFragger Glyco search excels at rapidly identifying glycopeptides, building on the open search methods developed in MSFragger. FragPipe allows this capability to be connected to the advanced methods for FDR control and quantitation available from other tools in FragPipe, enabling a complete platform for glycoproteomics. It also provides an easy way to integrate additional tools, such as the recently added O-Pair localization method that was originally implemented in MetaMorpheus.

Unlike other tools that are typically designed for either data-dependent acquisition (DDA) or data-independent acquisition (DIA) data, FragPipe can analyze both DDA and DIA data. To handle the complexity of DIA data, specific modules have been developed, including DIA-Umpire12, which demultiplexes spectra to pseudo-DDA spectra, and MSFragger-DIA, which directly searches multiplexed spectra. The search results are carefully curated to construct a spectral library, employing deep learning-based scoring and false discovery rate (FDR) filtering. This spectral library can be used to extract quantitative information from the DIA spectra. One of FragPipe’s key advantages is its ability to analyze DDA and DIA data together, which allows it to build a hybrid spectral library. Such a hybrid spectral library fully utilizes the information in both data types and contains more peptides, which results in more quantified peptides and proteins when used in library-based quantification.

Last but not least, FragPipe also has a command line interface that can be run on Linux servers, clusters, high-performance computers, etc. The GUI and the command line interface use the same codebase, which makes the result identical. The workflow files used to run the command line interface, and for saving settings in the GUI mode, are saved automatically whenever FragPipe is run and can be loaded to exactly reproduce a previous analysis. They can also be shared among users to provide easy access to developed methods and deposited with data uploaded to public repositories for reproducibility.

In summary, FragPipe is an all-in-one software tool that streamlines the entire process of mass spectrometry-based proteomics data analysis, from identification to quantification. Its ability to handle both DDA and DIA data types, support for glycopeptide identification and a wide variety of proteomics-associated workflows, and its ability to perform MS1-based and MS2-based quantification make it a versatile tool for researchers. FragPipe combines the user-friendliness of a commercial software program with the cutting-edge methods of research software to help improve data processing across bottom-up proteomics.

Figure 1. Graphical summarization of the modules and functionalities in FragPipe, which contains identification, quantification, PTM analysis, visualization, and downstream analysis.

Bios:

Fengchao Yu:

Fengchao is a research investigator from the Alexey Nesvizhskii Lab at the University of Michigan. His research interests include peptide identification, PTM discovery, label-free quantification, isotopic-labeling quantification, isobaric-labeling quantification, and DIA data analysis. Currently, Fengchao is the leading developer of FragPipe, MSFragger, and IonQuant. These tools have been used by research laboratories and companies in the United States and worldwide. He has also published papers in journals such as Nature Methods, Nature Biotechnology, Nature Communications, Molecular & Cellular Proteomics, and Journal of Proteome Research.

Daniel Polasky:

Daniel A. Polasky is a research investigator in the lab of Prof. Alexey Nesvizhskii in the department of Pathology at the University of Michigan. His research focuses on developing computational tools and methods for proteomics, with a particular focus on glycosylation and other post-translational modifications. He is a member of the MSFragger and FragPipe development teams, including leading work on MSFragger Glyco and associated tools for glycoproteomics data analysis. Before moving into computational proteomics, his PhD work in the lab of Prof. Brandon Ruotolo focused on developing mass spectrometry and ion mobility-mass spectrometry methods for analysis of intact proteins and protein complexes.

References:

Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat Methods 14, 513-520, doi:10.1038/nmeth.4256 (2017).
Yu, F. et al. Identification of modified peptides using localization-aware open search. Nat Commun 11, 4065 (2020).
Yu, F. et al. Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant. Mol Cell Proteomics 19, 1575-1585 (2020).
Käll, L., Canterbury, J. D., Weston, J., Noble, W. S. & MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nature Methods 4, 923-925, doi:10.1038/nmeth1113 (2007).
da Veiga Leprevost, F. et al. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nature Methods 17, 869-870, doi:10.1038/s41592-020-0912-y (2020).
Geiszler, D. J. et al. PTM-shepherd: Analysis and summarization of post-translational and chemical modifications from open search results. Molecular and Cellular Proteomics 20, 100018-100018, doi:10.1074/MCP.TIR120.002216 (2021).
Yu, F., Haynes, S. E. & Nesvizhskii, A. I. IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs. Molecular and Cellular Proteomics 20, 100077-100077, doi:10.1016/J.MCPRO.2021.100077 (2021).
Li, K., Vaudel, M., Zhang, B., Ren, Y. & Wen, B. PDV: An integrative proteomics data viewer. Bioinformatics 35, 1249-1251, doi:10.1093/bioinformatics/bty770 (2019).
Polasky, D. A., Yu, F., Teo, G. C. & Nesvizhskii, A. I. Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17, 1125-1132, doi:10.1038/s41592-020-0967-9 (2020).
Polasky, D. A., Geiszler, D. J., Yu, F. & Nesvizhskii, A. I. Multi-attribute Glycan Identification and FDR Control for Glycoproteomics. Molecular & Cellular Proteomics, doi:10.1016/j.mcpro.2022.100205 (2022).
Lu, L., Riley, N. M., Shortreed, M. R., Bertozzi, C. R. & Smith, L. M. O-Pair Search with MetaMorpheus for O-glycopeptide characterization. Nat Methods 17, 1133-1138, doi:10.1038/s41592-020-00985-5 (2020).
Tsou, C. C. et al. DIA-Umpire: Comprehensive computational framework for data-independent acquisition proteomics. Nature Methods 12, 258-264, doi:10.1038/nmeth.3255 (2015).

2023 HUPO ECR Manuscript Competition

Thu, 23 Mar 2023 22:01:34 GMT

Sponsored By: Expert Review of Proteomics by Taylor and Francis

Have you recently worked on an original manuscript in the field of proteomics? This is an excellent chance to participate in the 9th edition of the HUPO Early Career Researcher (ECR) Manuscript Competition at HUPO 2023 in Busan, South Korea. This is a unique opportunity for early career researchers to gain visibility in the proteomics community, as it highlights the important contributions that postdoctoral fellows, young clinicians and junior faculty members make to the proteomics field. Three finalists will be selected to present their manuscripts published during the 2022 and 2023 calendar years in a dedicated plenary session at HUPO 2023. An expert committee will evaluate the oral presentations to determine the “Proteomics Highlight of the Year”. The first-place winner will receive a cash prize of $1,000 USD and two runner-ups will each take home $500 USD, thanks to our sponsor, Expert Review of Proteomics by Taylor and Francis.

Application Deadline: April 15, 2023

More information and details can be found here.

32nd HUPO Human Brain Proteome Project Workshop

Thu, 23 Mar 2023 21:14:42 GMT

Date: May 21 - 23, 2023

Location: Sao Paolo, Brazil

The Human Brain Proteome Project (HBPP) launched in 2003 and was redesigned in 2015 to promote the connection of neuroproteomics scientists and actively encourage the inclusion of young investigators.

Our well-established annual HBPP workshop has been travelling around the world to capture, congregate, and connect the international neuroproteomics community.

This workshop will provide a forum for researchers to meet and discuss the latest developments in neuroproteomic research to better understand brain function and dysfunction.

Visit hbpp2023 for more information, program, speaker and registration details.

HUPO ECR Online Panel Discussion: Exploring Non-Academic Pathways in Proteomics

Thu, 16 Mar 2023 23:32:57 GMT

Join the Early Career Researcher (ECR) Committee for this exciting webinar!

DATE: Wednesday April 5, 2023

TIME: 10 am PDT / 12 noon CDT / 1 pm EDT

Are you interested in proteomics? Considering a non-academic career? Join the HUPO ECR Committee for their online panel discussion “Exploring Non-Academic Pathways in Proteomics”. The panel will have the following speakers:

Chris Rose (Scientist and Postdoc Mentor, Genentech)
Lindsay Pino (Co-founder and CTO, Talus Bio)
Maria Polychronidou (Senior Scientific Editor, Molecular Systems Biology, EMBO Press).

REGISTER HERE!

After registering, you will receive a confirmation email containing information about joining the webinar.

EMBO Practical Course: Characterisation of Post-Translational Modifications in Cellular Signalling

Sun, 12 Mar 2023 21:52:57 GMT

This EMBO practical course aims to provide a theoretical and practical overview of state-of-the-art techniques for the characterization of various PTMs, such as phosphorylation, acetylation, cysteine PTMs and glycosylation, and their cross-talking in controlling dynamic cellular mechanisms. The laboratory part will focus on a case study of EGF stimulated SILAC labeled HeLa cells. You will be introduced to enrichment, identification and quantitation of the PTM peptides and to mass spectrometry analysis as well as data interpretation and bioinformatics. This will provide you with knowledge needed to perform quantitative large-scale PTMomics from small amounts of sample material yourself. You will be taught in methods developed in the laboratories of the speakers and they will provide you with their own tips and tricks.

Course Location: University of Southern Denmark - Odense, Denmark

Course Date: June 15 June 22, 2023

Visit EMBO Practical Course website for more information.

HUPOST March 2023

Wed, 01 Mar 2023 20:19:25 GMT

The March HUPOST is now available. See HUPO 2023 updates, ECR Manuscript Competition info, ETC webinar and more!

WEBINAR: Career Advancement is Dependent on Paper Writing

Thu, 23 Feb 2023 21:20:12 GMT

Brought to you by the HUPO Education and Training Committee, the “ETC Auditorium-Stylish Academic Writing” professional development webinar series aims to help students and trainees improve their scientific writing skills. For the 3rd webinar, Prof. Ruedi Aebersold will share his views and experience regarding “scientific writing and publishing” and scientific communications. The presentation will highlight the importance of writing in a scientific career, comment on the scientific journal landscape and how to navigate it and discuss aspects of efficient scientific writing and common pitfalls.

DATE: Thursday, March 2, 2023

TIME: 10:00 am EST / 4:00 pm CET (Zurich) / 11:00 pm CST (Beijing)

SPEAKER: Prof. Ruedi Aebersold

PANELISTS:

Blandine Chazarin, Cedars-Sinai Heart Institute, Van Eyk Lab
Deepti Jaiswal Kundu, EMBL-EBI
Yansheng Liu, Yale University School of Medicine

REGISTER HERE in advance for this webinar. After registering, you will receive a confirmation email containing information about joining the webinar.

HUPOST February 2023

Sat, 04 Feb 2023 07:03:50 GMT

The February HUPOST is now available. See the latest info about the HUPO 2023 Congress, ECR and ETC activities, and more!

HUPOST January 2023

Wed, 11 Jan 2023 18:25:09 GMT

The January HUPOST is now available – it's a huge issue - chock full of news and information including farewell and welcome messages from HUPO Presidents, an ETC webinar, ECR Initiative recap of HUPO 2022, job opportunities and much, much more!

Welcome Message from President Jennifer Van Eyk

Tue, 10 Jan 2023 19:52:09 GMT

I am truly honoured and grateful to accept the role of HUPO President for the term 2023-2024. Thank you for the confidence placed in me and the entire HUPO Executive Committee (EC) team to continue to build our legacy. I also want to acknowledge the extraordinary leadership provided by Yu-Ju Chen and the previous HUPO Executive. Their work and dedication, particularly with the Strategic Plan, has moved the association into a new era. Together with the EC, I look forward to serving the HUPO membership and advancing a number of HUPO activities and initiatives.

HUPO boasts a number of distinctive strengths, namely the powerful passion and tireless work of its volunteers on various committees and initiatives with diversity and inclusion. These individuals together with HUPO’s management team, have realized a number of significant accomplishments over the past seven years including a 38% increase in financial assets, a 143% increase in membership, 122% increase in Industrial Advisory Board (IAB) members, highly successful virtual and in-person annual congresses, the digital HUPOST newsletter, implementation of the Proteomics Knowledge Resource (PKR), use of social media platforms, the establishment of the Early Career Researcher (ECR) Initiative and much more.

In looking to the future and how we can continue to build on our accomplishments, a Strategic Plan Working Group completed a thorough review of HUPO and focused on new aspirations that would create a better HUPO in the future. The most important aspirational goals were prioritized with the following major initiatives being developed to help attain these goals:

Expand the impact of proteomics in science.

Develop and enable HUPO ambassadors
Expand social media including the online presence of HUPO
Support the next phase of human proteome projects and other new initiatives
Collect and use “Success Stories” to support several goals

Bring the clinical world into HUPO and HUPO into the clinical world.

Outreach and support programs across translation and clinical applications

Support and facilitate education.

Create Best Practice recommendations for wet lab and dry (computational) lab workflows
Create and make available educational material and training courses
Expand outreach for educational programs outside the annual congress

Facilitate inclusive and diverse leadership at all levels of the HUPO organization.

Leadership training opportunities
Early and mid-career support for academia and industry paths

Improve the funding structure and mechanisms of the organization.

Every day, I am impressed by this extraordinary community that nurtures a culture of mutual care and international pride, and is dedicated to making life better for everyone who is touched by the work of thousands of individuals involved with proteomics. Each day, I see the brilliance, passion and commitment of so many and am inspired to continue strengthening and building this organization so it continues to flourish well into the future. HUPO has a remarkable story to tell, and I am eager to share it far and wide. I hope you will join me in continuing to propel HUPO and the proteomics community forward.

Sincerely,

Jennifer Van Eyk

HUPO President 2023-2024

Farewell from Past President Yu-Ju Chen

Tue, 10 Jan 2023 00:36:15 GMT

It was truly a great honor and an inspiring journey to serve as the HUPO President in the past two years. Looking back at the period of 2021-2022, the COVID-19 global pandemic continuously caused economic and social disruption, and seriously interrupted research projects, restricted travel and closed the borders of many countries, thus creating challenges for the congress organization and financial sustainability of HUPO.

“If you want to go fast, go alone. If you want to go far, go together." ~ African Proverb

When I started this unexpected journey two years ago, I was indeed full of worry if I was able to continue the previous great leadership in order to move forward and achieve transformative changes for the future of HUPO. I sincerely appreciate the great mentorship from past President Steve Pennington and past Vice President Susan Weintraub. At that time, I shared my firm belief that joint wisdom and collaborative efforts always inspire new ideas with success beyond the expectation of a single mind. It is truly admirable how passionate and committed many of the volunteers on HUPO committees and Council have been to the organization. The HUPO Executive Committee, all Committees, Council and HPP Executive Committee actively maintained the activities, expanded promotion worldwide and continued the research of the human proteome. For the benefit of members, HUPO continues to create new resources including the Proteomics Knowledge Resource (PKR), proteomics tutorial videos and stories from HUPO members. It is nice to see that HUPO is approaching a stable status with 1100+ members from 57 countries and 36 national societies.

Despite the pandemic challenges, somehow we learned to find a way to adapt to the environmental stress. Following the first HUPO Connect 2020 virtual congress, we had another successful virtual HUPO ReConnect 2021 with a record number of 1300 attendees. After two virtual meetings, we were finally able to meet each other and enjoy a great scientific program and fantastic social networking at the first in-person HUPO Congress in beautiful Cancun. A big thank you to Serio Encarnación-Guevara and Luis Manuel Teran who lead the Congress Organization Committee and the ICS team. Most importantly, it is the active participation of our members and great support from the industry sponsors who contributed to the congress's success with 900+ attendees.

Under the supervision of HUPO Treasurer Peter Hoffmann and joint efforts from past congress organizers, industry sponsors, HUPO members as well as the support from regional/national societies, available budget was directed to support future HUPO activities. The HUPO EC approved utilizing the available budget to formalize a way of supporting its committees and initiatives through funding requests.

In 2021, we celebrated HUPO’s 20th anniversary. To move forward with a modern version to advance proteome knowledge and accelerate proteomics research in the next 10 years, one of the most important tasks we completed in 2022 was the launch of the HUPO Strategic Plan. I take this opportunity to thank Secretary-General Henning Hermjakob, facilitator Ian Wright and the working group with representatives from HUPO EC, Committees, and the three regions who provided the final recommendations for education/training, increasing HUPO visibility, creating resources, improving funding, and external networking. Translating proteomics into utility, such as in the clinical community, is not a trivial issue. What we can really do for the next generation research, is to bridge both HUPO and the clinical community and partner with policy. The HPP Grand Project, aiming to explore the function of every protein, is the new phase of the HUPO Proteome Project and it is a great linkage to outreach to the global biomedical community.

Despite many successes in proteomics technology and discovery, there remains much to be done to demonstrate the value of proteomics to create benefits in our lives, such as clinical care, prevention medicine, precision agriculture, and food safety. I continue to encourage all HUPO members and everyone who loves proteomics from different parts of the world, to work together and create successful proteomics stories in the future.

Finally, I want to express my most sincere appreciation to Henning Hermjakob who has been the major driver to promote HUPO affairs, Chelsea Prangnell and Michele O’Bright from ICS to maintain the operation of the HUPO office during my term. I am also delighted to welcome the new leadership of President Jennifer Van Eyk and the new HUPO Executive Committee. In the Chinese zodiac, Rabbit is the symbol for 2023, representing smartness, speed, momentum and longevity. With Jennifer’s signature warmth, energy and passion, and the launch of the HUPO Strategic Plan, I would like to express my best wishes and look forward to fruitful achievements and growth of the HUPO community in 2023 and beyond.

Sincerely,

Yu-Ju Chen

HUPO Past President, 2021-2022

Webinar: The Essence of Data Visualization: How to Create Effective Figures of Your Data

Sat, 07 Jan 2023 05:18:00 GMT

The HUPO Education and Training Committee (ETC) presents: The Essence of Data Visualization: How to Create Effective Figures of Your Data

Date/Time: January 31, 2023 - 16:00-17:30 (Central European Time/Zurich)

Stimulated by a huge audience and feedback after the first ETC Auditorium on proteomics and academic writing, we are happy to announce our second speaker, Martin Krzywinski.

Martin Krzywinski works in bioinformatics, data visualization, science communication and the interface of science and art. He applies design, both data and artistic, to assist discovery, explanation and engagement with scientific data and concepts. Martin’s information graphics have appeared in the New York Times, Wired, Scientific American and covers of numerous books and scientific journals such as Nature and Genome Research. He is going to elaborate on how small changes to critical elements can turn a muddled figure into one that is clear and concise.

More about Martin: https://www.bcgsc.ca/martin-krzywinski-msc

Submit your figures and posters to Martin’ s dropline for redesign and discussion. The more you send in, the better. There are no bad figures, only figures waiting to be made better:

https://www.dropbox.com/request/usyBlym5FYO5ZOof0Agx

REGISTER HERE

HUPOST December 2022

Thu, 01 Dec 2022 19:13:08 GMT

The December HUPOST is now available – See the latest Congress information, news from ECR and MOC, a Humans of HUPO profile, research article, and much, much more!

Measuring protein turnover in animals using mass spectrometry

Thu, 24 Nov 2022 22:11:09 GMT

Written by Dr. Edward Lau and Dr. Rob Beynon

"A mouse has a new liver every few days, but the lifespan of a mouse liver cell is hundreds of days” - Dr. Rob Beynon

In 1965, Robert Schimke led a team that examined the response of rat liver tryptophan oxygenase (then called tryptophan pyrrolase, the first enzyme in the breakdown of the gluconeogenic amino acid tryptophan) to glucocorticoids and to feeding of the substrate, tryptophan [ref 1]. – both treatments led to elevated enzyme levels in the liver. They concluded that glucocorticoids induced synthesis of the enzyme, whereas dietary tryptophan prevented degradation - clear evidence of the importance of the two ‘opposing’ processes of synthesis and degradation controlling the intracellular abundance of an enzyme. This was, parenthetically, one of the first examples of a connection between the transcriptome (controlling synthesis) and the metabolome (controlling degradation).

This example serves to illustrate that despite the high energetic cost of making and degrading proteins, the proteome is in a dynamic state of renewal. Even in the steady state, where the protein abundance is constant, new proteins are synthesised and at the same time, the pool is commensurately depleted through degradation. This process of protein turnover can account for a sizeable proportion of the energy budget. The rate at which any protein is replaced must have evolved through natural selection; some proteins are replaced with minute time scales, others are essentially static through the life of the individual. Moreover, the rate of protein replacement is not the same in different tissues, nor is it the same in different species – smaller mammals, with a higher basal metabolic rate replace their proteins at much higher rates than larger mammals. Indeed, the high rate of protein turnover in small mammals may be a way to elicit thermogenesis.

Although the phenomenon of protein turnover has been described since the pioneering work of Schoenheimer eight decades ago, our knowledge of how it is regulated in homeostasis and disease and how it contributes to the anatomy and physiology of the proteome has remained lagging. Early studies, mostly using radioisotopes, could only measure turnover of total protein, and the goal of measurement of individual protein turnover rates seems unattainable

In recent years this has changed. Advances in separation science and mass spectrometry delivered the ability to resolve proteins, peptides or amino acids labelled with stable isotopes.

We and others would argue that we need to understand the scope and scale of intracellular protein turnover at the level of the proteome – it is likely that the subtlety seen by Schimke and colleagues is manifest in many other biological systems. Many protein turnover studies have been conducted with mammalian cells in culture. With this experimental system, it is relatively straightforward to introduce label isotopologs of essential amino acids into the cell culture media to trace their incorporation into proteins (dynamic SILAC approaches).

Although many insights have been gained from such studies in vitro, it is increasingly evident that turnover of proteins in cell culture is very different from that in large, intact adult animals. In rapidly growing cells protein synthesis is driven by high rates of cell proliferation, with doubling times of a day or less. By contrast, in intact animals the doubling rate of cells is measured in hundreds of days (for example, the mouse hepatocyte). At such a low proliferation rate, protein abundance cannot be adjusted by cell number expansion (with commensurate dilution), and individual proteins can be expected to be replaced in time frames that sit within the lifespan of the cell, ranging from minutes to that lifespan. To avoid proteotoxic aggregates, damaged proteins will need to be removed by carefully regulated degradation, rather than simply diluted to daughter cells. These two differences between cells in culture and in tissues require us to adopt different approaches and analytical strategies.

To properly understand the dynamics of the proteome, whether in steady state or in flux states, we need to measure protein turnover rates in intact animals. But, the convenience of a simple, instantaneous medium change no longer exists, and whole animal labeling studies require a different approach, confounded by difficulties of isotope administration and reutilisation of labeled amino acids for new protein synthesis. Moreover, turnover can only feasibly be accessed through measurement of synthesis by tracking incorporation of stable isotope labels. It is almost obligatory to measure the rate of synthesis of a protein through isotope incorporation, administered over days, months or years.

Quantification of protein turnover in animals is further complicated by the slow precursor availability in the tissue of interest after the isotopic label is administered. For example, labeled proteins or amino acids supplied in the diet have to move through the digestive system, cross the intestinal mucosal barrier, pass through the hepatic system and be transported to peripheral tissues in the blood. Any delay in appearance of labeled amino acids in the precursor pool of a peripheral tissue would interfere with measurement of the true turnover rate. By contrast, heavy water ([²H]₂O) crosses tissue barriers much more quickly. Thus, these two labelling methods could yield different apparent turnover rates for the same protein. But can the two approaches be brought to convergence? Intuitively, one would expect high turnover proteins to be most affected by slow precursor equilibration, and this is indeed the case.

In a recent study [ref 2], we compared two common methods of measuring protein turnover in animals either using heavy labeled amino acids in diet or provision of [²H]₂O in drinking water. The two strategies differ in precursor availability and metabolism, as well as the mass spectral features of peptides following label incorporation. Our question was very simple: what were the optimal data analysis strategies and when applied, do the two methods yield comparable turnover rate results?

We set up mouse labelling studies in which the only significant variable was the labeling protocol. Two groups of adult mice of identical strain, sex, age, maintained with identical husbandry, were labeled either with [¹³C₆]lysine or heavy water ([²H]₂O) over about a month. Animals were sampled at different times over this period, and the proteomes of the heart, liver, kidney, and skeletal muscle were analyzed by mass spectrometry. These tissues differ in their median turnover rate, allowing our analysis to extend over a broader range (liver and kidney are higher than heart, and in turn all three are higher than skeletal muscle). To ensure consistency in data processing, one of us (EL; https://ed-lau.github.io/riana) wrote Riana, new Python software that quantitates peptide labelling, recovers isotope abundance as a function of labelling time and fits these data to recover the first order rate of replacement, equivalent to steady state half-life.

Because heavy water is known to rapidly equilibrate across tissues and compartments, it would give data closest to the ground truth at least where label utilization is concerned. This experimental design therefore allows us to use water data as a reference for optimizing the analysis of lysine labelling data.

As anticipated, with [¹³C₆]lysine labeling there was a delay in precursor equilibration in all tissues. Simple exponential models of protein turnover are compromised by this delay, and the rate of turnover of high turnover proteins is underestimated. This can be corrected by using a suitable two-compartment kinetic model that also models the delay in the precursor pool, the protein turnover rate constant (k_d) and the precursor availability rate constant (k_d).

Surprisingly, finding suitable k_p values to adjust for labeling delay was not straightforward. Although the ratio of [¹³C₆]lysine vs. [¹²C₆]lysine can be measured in a tissue by LC-MS, an empirical sampling of tissue lysine isotope enrichment over time led to an apparent underestimation of the true precursor pool. Moreover, the best strategy for finding k_p is dependent on the tissue being examined. Global parameter optimization method can effectively find the best k_p value that explains the data sets in slow turnover tissues but is less effective in high turnover tissues. Therefore although the complications of slow precursor equilibration can be overcome with the proper strategy, careful considerations must be given based on the tissue and animal under study.

Such complications make a compelling case for heavy water as a turnover label in intact animals. Heavy water is inexpensive, virtually all peptides demonstrate isotopic incorporation, and the speed with which water equilibrates in the body mitigates complications due to precursor pool delay and reutilisation. That being said, heavy water is not without drawbacks. The pathways of heavy water labeling of different essential and non-essential amino acids is incompletely understood, and measurement of isotope incorporation in precursor spectra is more prone to errors and isobaric contamination in the mass spectra.

Accurate measurement of whole animal, proteome-wide protein turnover is still difficult, and there are several largely unresolved issues.

● What are the specific considerations in data analysis strategy when using different labeling protocols?

● Do existing analytical workflows and software packages give comparable turnover rates and profiles when analyzing a common data set?

● Each protein yields multiple peptides, and the rate of labeling of each peptide yields a measure of turnover. How are these data aggregated - is it better to combine all peptide data and fit once curve, or fit each peptide data individually? If the latter, are there objective criteria that can be applied to eliminate outlier turnover values?

● What are the optimal practices for error estimation in turnover measurements, and statistics in comparing turnover across conditions (e.g., homeostasis vs. disease)?

● Is it possible to establish a set of 'gold standard' turnover rates in different tissues and in different species?

We’d like to propose that those who are interested in this challenge bring together their knowledge and expertise in a community effort to resolve some of these questions. Should anyone be interested they are invited to contact us for further information.

Reference 1: Schimke et al. 1965 PMID 14253432

Reference 2: Hammond et al. 2022 PMID 35636728

Stylish Academic Writing Webinar

Thu, 24 Nov 2022 21:19:02 GMT

The goal of the “Stylish Academic Writing” professional development webinar series is to help students and trainees improve their scientific writing skills. The inaugural webinar was presented by Professor John Yates III from the Scripps Research Institute. Professor Yates is Editor-in-chief at the Journal of Proteome Research (JPR). This webinar covered different aspects of scientific writing, including Professor Yates’ personal approach to writing, how to make a perfect figure, and even how to manage disputes over authorship. In China alone, the webinar attracted nearly 3,000 online viewers even though it was aired close to midnight.

The title of Professor Yates’ presentation was "Write, Write, Write." Throughout the 45-minute presentation, Professor Yates shared several important tips including:
•   Develop a daily writing habit and try to publish often
•   Write manuscripts in small sections and paragraphs a little at a time
•   Don’t blindly accept changes. Instead, improve your writing by reviewing the stylistic and grammatical reasons behind each edit
•   Focus on the discussion section, which shows how your results advance the current understanding in the field
•   When choosing a journal to submit to, aim high, but choose appropriately
•   Seriously consider reviewer criticism to improve the quality of your paper

Professor Yates noted that writing is like working out in the gym. The more you do it, the stronger you get. As such, trainees should try to write often and publish everything they accomplish, no matter how small. Professor Yates discussed three pillars of academic writing: mechanics, style, and content.

With regards to mechanics and style, Professor Yates suggested that trainees read and pay attention to the writing of others. Proper grammar is essential to getting your message across and incorrect grammar can detract from your scientific content and can cause challenges to the review process. He recommends taking classes in English technical writing, using a copyeditor or software such as Grammarly, and to write frequently. He recommended “The Elements of Style” by Strunk and White as an excellent writing handbook.

Professor Yates discussed scientific content with respect to publishing in JPR. JPR prioritizes exciting, groundbreaking science, where studies are welcome from a wide swath of proteomic and metabolomic research. Publishable research requires proper statistical design for quantitative experiments. For this, he suggested reviewing a review article in JPR by Oberg and Vitek from 2009 (DOI: 10.1021/pr8010099). Studies should include enough samples and sufficient controls to properly power the experiment. Validation of biological experiments (including computational modeling) should be performed using experimental methods on independent patient or biological samples.

This session included an extended Q&A session with the audience, guided by Drs. Justyna Fert-Bober (Cedars Sinai, USA), Tiannan Guo (Westlake University, China) and Brian Searle (Ohio State University, USA). A full video recording of the session including the Q&A session is available on the HUPO Proteomics Knowledge Source website (https://pkr.hupo.org/).

HUPOST November 2022

Thu, 03 Nov 2022 00:05:32 GMT

The November HUPOST is now available - there's a ton of news and information in this issue including HPP Day, B/D-HPP article and Twitter Poll, ECR events and activities, Humans of HUPO profile, job opportunities and much, much more!

The Impact of Real-time Mass Spectrometry Data Analysis on the Field of Proteomics

Wed, 02 Nov 2022 01:22:01 GMT

Authors:

Yun-En Chung¹ and Mathieu Lavallée-Adam¹

¹Department of Biochemistry, Microbiology and Immunology and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada

Mass spectrometry-based proteomics data analysis has never been more exciting. The combination of computational hardware improvements and a wide diversity of instruments and experimental techniques has created a gigantic playground for computational researchers and software developers. In recent years, one attraction at this playground has gained a lot of attention from both academia and industry: real-time analysis of proteomics data.

In a traditional mass spectrometry-based proteomics experiment, tens of thousands of mass spectra are collected for a biological sample. After the conclusion of the experiment these mass spectra are then inputted into software packages for peptide and protein identification and quantification. Hence, since biological information is inferred solely through post-hoc analysis, the mass spectrometry experiment is mostly running blind and does not adapt in real-time based on the biological data that is being acquired.

Improvements in computational hardware and the recent availability of Application Programming Interfaces (APIs) enabling mass spectrometry data analysis during proteomics experiments have paved the way to the design of a new family of algorithms and software packages performing the real-time analysis of mass spectrometry data. Tools such as the Thermo Fisher Scientific Instrument API (IAPI)¹ and the Bruker Parallel database Search Engine in Real-time (PaSER)² are enabling the design of analyses that accelerate data processing, help diagnose problems with instrumentation and enhance the characterization capabilities of mass spectrometry.

One of the early modern applications of real-time mass spectrometry data analysis is the on-the-fly quality assessment of mass spectrometry experiments. Instrument performance drop or malfunction are often only identified after post-hoc data analysis. Such a late discovery results in a waste of time and resources that are used to acquire unusable or subpar data. The QC-ART approach³ has been developed to evaluate instrument performance in near real-time and allow for immediate intervention. QC-ART ensures consistent high-quality data collection and the rapid detection of instrumentation problems.

Since the early beginnings of mass spectrometry-based proteomics, data acquisition remained an extremely active research topic. Still today, new acquisition techniques are being developed to supplement the current families of approaches including data-dependent acquisition⁴, data-independent acquisition⁵ and targeted methods^6,7. Traditionally, an instrument would apply the same acquisition strategy (precursor ion selection algorithm, scan window size, …) for the entirety of an experiment. This standard acquisition method works reasonably well in common proteomics use cases. However, since the instrument does not consider the biological relevance of the data it is acquiring, a significant proportion of this data does not translate into meaningful biological discoveries.

An excellent example of this is how real-time database search for peptide identification can support the selection of peptides for quantification with isobaric labeling. It was previously shown that MS3 spectra lead to more accurate quantification using tandem mass tag reporter ions than MS2 spectra⁸. However, acquiring MS3 spectra is resource intensive. It is therefore important to acquire MS3 spectra for data that is biologically relevant. Orbiter was therefore developed to identify peptides in real-time from MS2 spectra with a database search method⁹. Orbiter then only acquires MS3 spectra from MS2 spectra that yield a confident peptide identification and therefore optimizes resource usage for protein quantification.

Other groups developed software packages to identify peptides in real-time^10,11, while McQueen et al. presented a pseudo real-time approach that paused the experiment to adjust future data acquisition based on such peptide identifications. Inspired by these methods, our team proposed that the real-time identification of peptides and proteins can be used to guide mass spectrometry data acquisition in order to optimize resource usage and maximize protein identifications. Indeed, our computational approach, named MealTime-MS¹², uses real-time database search to identify peptides and supervised learning to assess the confidence of protein identifications. MealTime-MS then uses confident protein identifications to generate an exclusion list preventing the acquisition of tandem mass spectra for peptide ions that are expected to belong to proteins that were already identified in the mass spectrometry run. MealTime-MS showed that up to 33% of the mass spectra collected in traditional experiments could be safely ignored with minimal losses of proteins identified compared to standard experiments and that these mass spectra could be repurposed for the identification of additional proteins.

Alternatively, real-time analysis of mass spectrometry data has demonstrated its utility in targeted proteomics. In a typical targeted proteomics experiment, specific elution time windows need to be determined for targeted peptides. Due to run-to-run technical variation, the size of these scheduled windows must be kept relatively large to ensure the instrument encounters these peptides, thereby limiting the number of possible targets. MaxQuant.Live presented a solution via real-time recognition of precursor ions¹³. The algorithm uses the retention time, mass-to-charge ratio, and intensity of the precursor ions encountered to predict and therefore select those that should be targeted for quantification. This approach enabled the targeting of over 25,000 peptides in a single mass spectrometry run.

Real-time analysis of mass spectrometry-based proteomics data has also demonstrated its clinical applications. Devices such as the MasSpec Pen demonstrated how a small handheld device can be used to rapidly detect features including lipids, metabolites and proteins in human tissue. Such features can be used as biomarkers to diagnose in real-time whether tissues are cancerous or healthy.

After reading about these applications, we would like you to join the conversation on Twitter by answering our poll question here and letting us know where the future of real-time proteomics data analysis sits:

Twitter Poll:

In which area do you think real-time analysis of mass spectrometry-based proteomics data will have the greatest impact in the future:

Protein ID
Protein Quantification
Clinical Applications
Other (write in replies)

Figure 1. Graphical representation of the traditional mass spectrometry-based proteomics pipeline, where acquired data is analyzed after the completion of the experiment and of a pipeline integrating real-time data analysis to adjust mass spectrometry data acquisition during the experiment.

Computer Icon created by Freepik - Flaticon: https://www.flaticon.com/free-icons/course.

Bios:

Yun-En Chung:

Yun-En Chung is an undergraduate student in Translational and Molecular Medicine and researcher in Dr. Mathieu Lavallée-Adam’s lab at the University of Ottawa. His research focuses on the development of software packages to guide mass spectrometry experiments in real-time to improve data acquisition efficiency. His publication on the real-time identification of proteins in mass spectrometry data was recognized as the best paper from a Master’s or Undergraduate student at the Ottawa Institute of Systems Biology in 2020. He also received several awards for his presentations, including a 2^nd place for his oral presentation at the Undergraduate Research Opportunities Program Seminar day at the University of Ottawa and an honorable mention for his poster at the American Society for Mass Spectrometry annual conference in 2022. Yun-En’s research is funded by awards from the Natural Sciences and Engineering Research Council of Canada and Mitacs.

Mathieu Lavallée-Adam:

Mathieu Lavallée-Adam is an Associate Professor at the University of Ottawa in the Department of Biochemistry, Microbiology and Immunology and is affiliated to the Ottawa Institute of Systems Biology. He obtained a B.Sc. in Computer Science and a Ph.D. in Computer Science, Bioinformatics option, from McGill University and performed his postdoctoral research at The Scripps Research Institute. His research focuses on the development of statistical and machine learning algorithms for the analysis of mass spectrometry-based proteomics data and protein-protein interaction networks. Dr. Lavallée-Adam is a recipient of the John Charles Polanyi Prize in Chemistry, rewarding the impact of his bioinformatics algorithms on the mass spectrometry community and was named Early Career Researcher of the Year by the Ottawa Institute for Systems Biology in 2021. He is also Co-Chair of the HUPO Early Career Researcher Initiative and a member of the HUPO Executive Committee, in which he develops training activities and advocates for junior investigators in proteomics and organize events highlighting their research on the international stage.

References:

1. Scientific, T. F. Thermo Fisher Scientific IAPI GitHub. (2022). Available at: https://github.com/thermofisherlsms/iapi.

2. Bruker. PaSER 2022. (2022).

3. Stanfill, B. A., Nakayasu, E. S., Bramer, L. M., Thompson, A. M., Ansong, C. K., Clauss, T. R., Gritsenko, M. A., Monroe, M. E., Moore, R. J., Orton, D. J., Piehowski, P. D., Schepmoes, A. A., Smith, R. D., Webb-Robertson, B.-J. M., Metz, T. O. & TEDDY Study Group. Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data. Mol. Cell. Proteomics 17, 1824–1836 (2018).

4. Liu, H., Sadygov, R. G. & Yates, J. R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193–201 (2004).

5. Venable, J. D., Dong, M.-Q., Wohlschlegel, J., Dillin, A. & Yates, J. R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 1, 39–45 (2004).

6. Kuhn, E., Wu, J., Karl, J., Liao, H., Zolg, W. & Guild, B. Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics 4, 1175–86 (2004).

7. Anderson, L. & Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5, 573–88 (2006).

8. Ting, L., Rad, R., Gygi, S. P. & Haas, W. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 8, 937–40 (2011).

9. Schweppe, D. K., Eng, J. K., Yu, Q., Bailey, D., Rad, R., Navarrete-Perea, J., Huttlin, E. L., Erickson, B. K., Paulo, J. A. & Gygi, S. P. Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics. J. Proteome Res. 19, 2026–2034 (2020).

10. Bailey, D. J., Rose, C. M., McAlister, G. C., Brumbaugh, J., Yu, P., Wenger, C. D., Westphall, M. S., Thomson, J. A. & Coon, J. J. Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc. Natl. Acad. Sci. U. S. A. 109, 8411–6 (2012).

11. Graumann, J., Scheltema, R. A., Zhang, Y., Cox, J. & Mann, M. A framework for intelligent data acquisition and real-time database searching for shotgun proteomics. Mol. Cell. Proteomics 11, M111.013185 (2012).

12. Pelletier, A. R., Chung, Y.-E., Ning, Z., Wong, N., Figeys, D. & Lavallée-Adam, M. MealTime-MS: A Machine Learning-Guided Real-Time Mass Spectrometry Analysis for Protein Identification and Efficient Dynamic Exclusion. J. Am. Soc. Mass Spectrom. 31, 1459–1472 (2020).

13. Wichmann, C., Meier, F., Winter, S. V., Brunner, A.-D., Cox, J. & Mann, M. MaxQuant.Live enables global targeting of more than 25,000 peptides. bioRxiv 443838 (2018). doi:10.1101/443838

HUPO ECR Online Panel: Science Communication - Who, How, Where and Why?

Tue, 01 Nov 2022 17:28:33 GMT

Join the next online panel hosted by the HUPO Early Career Researcher (ECR) Initiative on November 16th at 4PM GMT for a discussion on 'Science communication - who, how, where, and why?'. We have three wonderful panelists:

Dr. David Tabb, Institut Pasteur
Dr. Ann Van der Jeugd, Leuven Brain Institute
Dr. Ben Orsburn, Johns Hopkins University

Effective science communication has ripple effects through all aspects of society. But how do you convey clear and concise messages? What is the best way to get these messages across a wide range of platforms? Get the answers to all these questions and more!

REGISTER HERE in advance for this webinar.

After registering, you will receive a confirmation email containing information about joining the webinar.

HUPO Webinar Series: STYLISH ACADEMIC WRITING

Wed, 26 Oct 2022 07:53:54 GMT

The HUPO Education and Training Committee (ETC) webinar series is intended to help you organize and write a quality academic research paper. We will present how to polish academic style, how to manage data presentation, and how to learn from critical reading. Our mission is to provide academic support to strengthen student learning and empower every student to develop as self-academic writer whose work is admire.

Date: November 2, 2022
Time: 8:00 am PST

WEBINAR LINK: https://us06web.zoom.us/j/84142263041

Speaker: John Yates III, PhD, Professor, Department of Molecular Medicine, Editor of Journal of Proteome Research. Dr. Yates research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and biological studies involving proteomics. Additional to thousands of publications, international and national awards, and recognitions, Dr. Yates served as an Associate Editor at Analytical Chemistry for 15 years and is currently the Editor in Chief at the Journal of Proteome Research.

HUPO B/D-HPP Single Cell Initiative Webinar - October 26, 2022 - REGISTER TODAY!

Sat, 15 Oct 2022 20:30:23 GMT

See our exciting program information below. REGISTER TODAY!

All times are US Eastern Time.

10:00 am Matthias Mann, "Ultra-high sensitivity for precision oncology"

10:30 am Erwin Schoof, "Leveraging advanced latest-generation acquisition and MS instrument architecture for improving single cell proteomics experiments"

11:00 am Roman Zubarev, "Since cell proteomics - some considerations from the chemical proteomics point of view"

11:30 am Claudia Ctortecka, "Variations of the proteoCHIP - a high-throughput sample preparation approach for single-cell proteomics"

12:00 pm Ying Zhu, "Enhancing single cell proteomics and tissue proteome mapping with ion mobility filtering"

12:30 pm Ryan Kelly, "Advanced separations and data acquisitions strategies for in-depth single-cell proteomics"

13:00 pm Closing remarks

REGISTER HERE!

Organized by the B/D-HPP Single Cell Initiative. Please contact Initiative Chair Dr. Bogdan Budnik (Bogdan.Budnik@wyss.harvard.edu) with any questions or if you want more info!

HUPOST October 2022

Wed, 12 Oct 2022 19:31:21 GMT

Check out the October issue of HUPOST here, full of the latest news and updates, including HUPO's Strategic Plan!

The HUPO ECR Initiative is Proud to Welcome a New Member - Dr. Saeed Seyedmohammad

Mon, 03 Oct 2022 23:23:46 GMT

Dr. Seyedmohammad started off his career in immunology where he Investigated Inhibitory signals at the T-cell Immune Synapse. During his master’s degree at Imperial College London, he developed important immune assays that helped in the identification of prominent signaling molecules involved in T-cell activation. He then obtained his doctoral degree in biochemistry at the University of Cambridge, where he studied the characterization of a bacterial iron transport protein from Pseudomonas aeruginosa. In that thesis, Dr. Seyedmohammad successfully proved the trimeric conformation of the protein and identified key binding motifs driving the acquisition of iron into the bacterial cell. After venturing into several start-ups, he began a post-doctoral fellowship under the supervision of Dr. Van Eyk at the Advanced Clinical Biosciences Research Institute in Cedars Sinai Medical Research Division, where he is currently using novel proteomic approaches to study heart failure. Dr. Seyedmohammad is responsible for identifying newly synthesized proteins in human cardiomyocytes using AHA-labeling and is applying this approach to characterize important protein pathways involved in heart disease as a consequence of ischemia and reperfusion. He is also responsible for developing high-throughput assays, using a COVARIS sonication system to scale-up sample processing for a robust workflow.

HUPOST September 2022

Tue, 06 Sep 2022 20:14:25 GMT

The September HUPOST is now available! Lots of exciting and interesting info - Congress updates, EC Elections, ECR News, B/D HPP info and more!

HUPO B/D-HPP Single Cell Initiative Webinar - October 26, 2022 - Mark Your Calendar!

Tue, 06 Sep 2022 18:12:25 GMT

See our exciting program information below. All times are US Eastern Time.

10:00 am Matthias Mann, "Ultra-high sensitivity for precision oncology"

10:30 am Erwin Schoof, "Leveraging advanced latest-generation acquisition and MS instrument architecture for improving single cell proteomics experiments"

11:00 am Roman Zubarev, "Since cell proteomics - some considerations from the chemical proteomics point of view"

11:30 am Claudia Ctortecka, "Variations of the proteoCHIP - a high-throughput sample preparation approach for single-cell proteomics"

12:00 pm Ying Zhu, "Enhancing single cell proteomics and tissue proteome mapping with ion mobility filtering"

12:30 pm Ryan Kelly, "Advanced separations and data acquisitions strategies for in-depth single-cell proteomics"

13:00 pm Closing remarks

REGISTER HERE!

Organized by the B/D-HPP Single Cell Initiative. Please contact Initiative Chair Dr. Bogdan Budnik (Bogdan.Budnik@wyss.harvard.edu) with any questions or if you want more info!

The HUPO Early Career Researcher Initiative Welcomes a New Member: Livia Rosa

Fri, 02 Sep 2022 01:28:38 GMT

Livia Rosa-Fernandes is part of Prof. Marinho’s research team at The Institute of Biomedical Sciences of the University of São Paulo and a Research Fellow in Neuroproteomics at Macquarie University Centre for Motor Neuron Disease Research. She received her Ph.D. in Medical Sciences from USP Medical School (2015). During her Ph.D., she had the opportunity to work at Brigham and Women´s Hospital-Harvard Medical School (USA), as part of the Postgraduate Research Exchange Program. In 2016, Livia moved to Denmark, where she worked as a post-doctoral researcher both at the Department of Biochemistry and Molecular Biology and the Institute of Molecular Medicine, at the University of Southern Denmark. From 2019, she was enrolled as a post-doctoral fellow at the Institute of Biomedical Sciences, USP (Brazil).

Over time, Livia has gathered experience using in vivo and in vitro models together with molecular tools to study biological processes focusing on disease progression, cellular communication, and its microenvironment. MS-based proteomics and data analytics play a key role in her research as powerful tools to better understand a biological event. Her scientific production reflects an effort to engage in multidisciplinary fields and strengthen a collaborative approach to science. She is also part of the Brazilian Proteomics Society council and is engaged in several initiatives to promote knowledge transfer and increase access to scientific education.

Celebrating Outgoing and Welcoming Incoming B/D-HPP Executive Committee Members

Fri, 02 Sep 2022 01:19:34 GMT

With the recent refresh of the HUPO Biology/Disease-driven Human Proteome Project (B/D-HPP) Executive Committee, we took the opportunity to get the thoughts of several members of the committee who completed their tenure. Drs. Corrales, Deutsch, Omenn, and Schmidt have all given their valuable time and leadership to the HUPO mission and have been critical to the continued growth of the B/D-HPP initiatives and the continued adoption of proteomics advances toward understanding pressing questions in health and life sciences. We asked them what they would like to share with the HUPO community on this occasion.

Dr. Fernando Corrales served as co-chair, chair, and past-chair of the B/D-HPP from 2015–2021. As the Human Liver Proteome Project (HLPP) chair, he also has led the HLPP since 2014. Regarding what he sees as the importance of the B/D-HPP at large, the former chair said that it has represented to him an “opportunity to translate the essence of proteomics” and particularly into “functional understanding of biological systems.” Dr. Corrales, who is Professor at the Spanish National Centre for Biotechnology, sees the B/D-HPP as the masterpiece of the upcoming Grand Project once it is integrated with the other resources of the HPP. The experience sharing the coordination of the B/D-HPP with Drs. Jenny van Eyk and Ileana Cristea has been outstanding and the efforts of all persons on board during these years have been generous, says Dr. Corrales.

“Defining protein function is something clearly dependent on the biological environment where proteins develop their activity and B/D Teams integrate an ideal research network to dissect so far hidden functionalities and place them into the adequate physiological and/or pathological framework." – Fernando Corrales

Dr. Eric Deutsch, who served on the executive committee for five years, agrees on the importance of ensuring B/D-HPP initiatives receive continued community support. “I wish the new committee well in working to increase active participation of all B/D-HPP initiatives”, adds the longtime HUPO leader and Principal Scientist at the Institute of Systems Biology.

Dr. Gil Omenn is the Harold T. Shapiro Distinguished University Professor at University of Michigan and a longtime chair of the HUPO Human Proteome Project (HPP). He served on the B/D-HPP executive committee for a decade alongside Drs. Ruedi Aebersold, Jenny van Eyk, Fernando Corrales, Ileana Cristea, and now Nicki Packer as chairs, and chaired the Human Plasma Proteome Project from the launch of HUPO in 2002. Under his leadership, the Plasma, Brain, Liver, Cancer, and Cardiovascular Proteome Projects were brought together with many emerging projects to form the B/D-HPP in 2011 and join the Chromosome-centric C-HPP in the HUPO HPP. This year, Dr. Omenn has rotated off the B/D-HPP executive committee after a successful term that saw him continue to lead the executive committee with his vision, which culminated in an HPP Metrics of the Human Proteome paper in the annual special issues of the Journal of Proteome Research[1] and a special perspective article in Molecular & Cellular Proteomics[2].

“The B/D-HPP teams have made important contributions to the global explosion of research utilizing proteomics to reveal pathways, networks, mechanisms, and biomarkers underlying a great range of biological processes and diseases,” – Gil Omenn

Dr. Frank Schmidt is an active leader in the B/D-HPP community and served on the executive committee. As his term concludes, Dr. Schmidt said he will remember his time with the committee “very positively”. The transition to the digital age during the COVID-19 pandemic was especially memorable, "when we successfully held our first professional webinars and were able to push new ideas under the excellent leadership of Ileana [Cristea] and Fernando [Corrales]”, reminisces Dr. Schmidt, who is Professor at Weill Cornell Medicine-Qatar. He wishes the new committee good luck as a new crop of members from the proteomics community continue the initiative missions.

We look forward to continuing the work of the HUPO B/D-HPP in engaging the proteomics community and promoting the adaption of proteomics advances toward life and medical sciences. We welcome the new and continuing HUPO B/D-HPP Executive Committee members for 2022–2023:

Dr. Michal Bassani, Immunopeptidomics, continuing
Dr. Bogdan Budnik, Single cell proteomics, new
Dr. Ferdinando Cerciello, Cancer, continuing
Dr. Ileana Cristea (Co-chair/Past Chair), Infectious disease, continuing
Dr. Ruth Huttenhain, Signaling and protein networks & ECR, new
Dr. Maggie Lam, Cardiovascular, continuing
Dr. Ed Nice, Cancer, new
Dr. Aleksandra Nita-lazar, Infectious disease, continuing
Dr. Nicki Packer (Chair), Glycoproteomics, continuing
Dr. Uwe Völker, Clinical proteomics, new

Footnotes:

[1] Omenn GS et al. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res. 2020 Dec 4; 19(12): 4735–4746. PMID: 32931287

[2] Omenn GS. Reflections on the HUPO Human Proteome Project, the flagship project of the Human Proteome Organization, at 10 years. Mol Cell Proteomics. 2021 Feb 26;20:100062. PMID: 33640492.

Recent Developments in MSstats Ecosystem: A collection of statistical methods for general scalable quantitative analysis of proteomic experiments

Fri, 02 Sep 2022 01:12:46 GMT

Devon Kohler¹, Mateusz Staniak⁴, Olga Vitek¹

¹Khoury College of Computer Science, Northeastern University, Boston, MA, USA; ⁴University of Wroc law, Wroc law, Poland

The MSstats ecosystem is a family of open-source R/Bioconductor packages implementing statistical methods for quantitative mass spectrometry-based proteomic experiments. Here we review its recent developments, as well as advances in previously available methods and implementations.

Read full article here.....

HUPOST August 2022

Wed, 03 Aug 2022 23:54:30 GMT

The August HUPOST is here! See the latest info about the HUPO 2022 World Congress, Education and Training Committee (ETC) activities, ECR Initiative and an update from the HPP.

HUPOST July 2022

Tue, 05 Jul 2022 05:50:40 GMT

The July HUPOST is now available! Be sure to have a look at the HUPO 2022 World Congress updates, ECR and MOC news, Humans of HUPO and Job Opportunities!

HUPOST June 2022

Thu, 02 Jun 2022 16:48:27 GMT

The June HUPOST is now available....See important information about HUPO's Statement on Ukraine, World Congress, Awards Deadline, ETC and ECR updates....and much more!

HUPO Education and Training Committee Welcomes New Members

Tue, 31 May 2022 14:34:57 GMT

Blandine Chazarin, PhD is currently a postdoctoral scientist in Jennifer Van Eyk's lab at Cedars-Sinai Medical Center in Los Angeles (CA, USA). Previously she studied biology at Paul Sabatier University (Toulouse, France) prior advanced training in proteomics and mass spectrometry at Lille 1 University (Lille, France). She obtained a PhD using mass spectrometry to better understand hibernating brown bear physiology to path the way of therapeutic against muscle atrophy at LSMBO (Strasbourg, France). She is the former president of the youth club of the proteomic French Society and organized yearly meeting dedicated to young scientists in proteomics. Now, she is involved in postdoctoral scientist society at Cedars-Sinai and developed single cell proteomic approach applied to cardiac cells proteome analysis.

Vision for ETC: Being an early career scientist can be challenging and Universities are not teaching how to evolve in science. It’s time to form our next generations of scientists by sharing trainings, advertising incoming meetings and provide additional information about grants and networking.

Ben Collins, PhD is currently a Reader (equiv. Assoc. Prof.) in the School of Biological Sciences, Queen’s University of Belfast, UK (since 2019). His research focuses on broadly on 3 topics: (i) method development and applications in data independent acquisition mass spectrometry; (ii) method development and applications in the analysis of protein interaction networks and protein complexes; and (iii) applications of these strategies in host-pathogen biology and innate immunity. Ben Collins’s PhD was completed at University College Dublin in 2009 where he remained for 1 year as the Agilent Technologies Newman Fellow (postdoctoral) in Quantitative Proteomics. He moved to the Institute of Molecular Systems Biology at ETH Zurich in Autumn 2010 as postdoctoral researcher under the supervision of Prof. Ruedi Aebersold, where his research focused on the application of quantitative interaction proteomics in signaling and the development of DIA/SWATH mass spectrometry. Following this Ben Collins was a Group Leader and SNF Ambizione Fellow at IMSB, ETH Zurich with a focus on applying methods developed as a postdoc to relevant problems in host-pathogen biology.

Vision for ETC: Training and education are at the heart of HUPO activities, so I am excited to be involved in the effort to revitalize this initiative. My view is that there are many high-quality educational activities ongoing organized by independent groups and a part of our effort should be to make people aware of these courses in an organized way, and to distribute videos/materials as widely as possible where available. We should also aim to complement the current offerings with HUPO-organized courses on prioritized topics. Key to our success will be to reach proteomics-focused scientists but also beyond into the broader life science community where we can have tremendous impact.

Deepti Jaiswal Kundu, PhD works as a Scientific Curator at EMBL-EBI, Cambridge, UK. Before joining EMBL-EBI, she studied botany, psychology, and bioinformatics in India, before doing a PhD in Cheminformatics in the Czech Republic. After successfully defending her thesis in 2015 Deepti Jaiswal Kundu moved to Cambridge, UK and took a break of briefly 2 years to have daughter. She joined EBI in 2018. As a Scientific Curator, Deepti Jaiswal Kundu is responsible to check and validate new datasets submitted to the PRoteomics IDEntifications Database (PRIDE) - the world’s largest public database dedicated to mass spectrometry-based proteomics. Furthermore, she curates the datasets for further reanalysis and integration to other bioinformatic resources in EBI.

Vision for ETC: I would like ETC to reach more people and encourage students/scientists to participate in training programs, conferences, and meetings.

Qingsong Lin, PhD is a Principal Research Fellow (Research Associate Professor) of the Department of Biological Sciences, National University of Singapore (NUS). He is the Director of the Protein and Proteomics Centre (PPC), NUS. Besides, he is the President of the Singapore Society for Mass Spectrometry (SSMS) since 2017. His expertise lies in applications of mass spectrometry in proteins and proteomics, extended to other biomolecules. His research interests are mainly in disease biomarker discovery and disease mechanism, drug target identification and mechanism of action studies, as well as the application of mass spectrometry and quantitative proteomics technologies to address various biological questions.

Vision for ETC: To grow HUPO ETC as the world’s most comprehensive proteomics resource; to educate and train proteomics scientists from fundamental to advanced levels.

Yansheng Liu, PhD is an Assistant Professor in the Department of Pharmacology at Yale University School of Medicine. His research group is interested in DIA-MS and has combined DIA with SILAC and phosphoproteomics for studying fundamental biological questions in cell signaling.

Vision for ETC: I believe the new HUPO ETC should engage the next generation of scientists and is eager to organize workshops in which young scientists, such as first-authors in manuscripts, can present and learn from each other.

Brian Searle, PhD is an Assistant Professor at the Ohio State University Medical Center in the Department of Biomedical Informatics and a member of the Pelotonia Institute for Immuno-Oncology (PIIO). Brian received his chemistry BA at Reed College in 2001. In 2004, he co-founded Proteome Software with Mark Turner and Dr. Ashley McCormack to produce and distribute cutting-edge data analysis software for proteomicists. In 2014, he returned to academia to earn his PhD with Dr. Michael MacCoss at University of Washington, where he developed methods to detect and quantify proteins and phosphosites using mass spectrometry. His lab at PIIO spans the intersection of proteomics, mass spectrometry, bioinformatics, and technology development to study human genetic variation in the backdrop of cancer.

Vision for ETC: I am excited to see the ETC produce the best available educational resources for proteomicists of all skill levels to learn new technologies, and to give early-career proteomicists a chance to interact with top-level researchers and grow their careers.

Low Teck Yew, PhD is an associate professor and senior research fellow located at the UKM Medical Molecular Biology Institute (UMBI) which is affiliated to the National University of Malaysia (UKM), leading the cancer proteomics and metabolomics group. Before that, he worked at Netherlands Proteomics Centre (NPC) in Utrecht University in the Netherlands. His research interests include bridging (phospho)proteomics with clinics and cancer proteogenomics.

Vision for ETC: I hope to connect researchers in southeast Asia (SEA) to the international community in proteomics research and enhance the exposure of this region with respect to education and training. I also wish to share some of the special research topics in this region, which has its own rich and unique biodiversity, to international researchers.

Join the HUPO ECR Initiative for a Panel Discussion on Scientific Collaboration!

Tue, 31 May 2022 05:49:12 GMT

The HUPO Early Career Researcher (ECR) Initiative is an international community of early career researchers in proteomics, whose mission is to provide networking and career development opportunities for aspiring researchers. To help achieve this, the ECR Initiative organizes panel discussions to foster professional development and a space for mentorship. In the upcoming panel discussion, we will be covering the topic of scientific collaborations.

Scientific collaborations can bridge disciplines, expertise, and countries to produce innovative research. Certainly, the COVID-19 pandemic has highlighted the importance of collaborating and has also changed the way scientists across various disciplines collaborate. But how do you collaborate successfully and effectively?

Join us on Wednesday June 29th at 10:00PM GMT for the HUPO ECR online panel discussion, "Choosing and Managing Collaborations: The Do's and Don'ts". We will be joined by three experienced collaborators who will share valuable lessons learned on collaborating:

Dr. Vera Ignjatovic – Murdoch Children's Research Institute, Australia
Dr. John R. Yates III – Scripps Research, USA
Dr. Jennifer Geddes-McAlister – University of Guelph, Canada

They will be sharing their input on how to have a successful career of collaborations. You won’t want to miss it!

REGISTER HERE

HUPO Condemns Invasion of Ukraine

Mon, 09 May 2022 16:14:00 GMT

The Human Proteome Organization (HUPO) condemns, in the strongest terms, the military invasion of Ukraine by the Russian Federation, and deplores the resulting loss of life and humanitarian impact.

We urge all HUPO members to offer opportunities for support, scientific research and collaboration to Ukrainian scientists, whether abroad, displaced or under threat in their home country, and recommend highlighting these opportunities through HUPO channels as well as portals like https://scienceforukraine.eu/.

As a global scientific organisation, HUPO supports the principles of the universality of science (https://council.science/5-universality-of-science). It is therefore key to note that our colleagues in Russia will maintain their individual positions and roles within HUPO, and will continue to have, as individuals, full access to all HUPO information and activities. Indeed, as a scientific organisation, with engagement, inclusivity, and transparency at our core, we do not condone any actions by anyone against any individuals simply because of their country of origin or residence.

HUPOST May 2022

Mon, 02 May 2022 22:59:37 GMT

The May HUPOST is now available! Check out lots of interesting info and articles...

HUPOST April 2022

Tue, 05 Apr 2022 23:26:43 GMT

April HUPOST is now available -- Catch all the important info and updates!

C-HPP Workshop - Algarve, Portugal

Sat, 02 Apr 2022 00:02:08 GMT

On Friday, May 13, following the 3-day 2nd Joint Meeting of Spanish, French and Portuguese Proteomics Societies, the Chromosome Centric Human Proteome Project (C-HPP) announces the 25th C-HPP Workshop on “Accelerating the HPP Grand Challenge”.

This satellite workshop is open and free to all participants of ProteoVilamoura. Agenda: https://www.hupo.org/News/12690881

If you want to attend, just register on our website: https://proteo-vilamoura.sci-meet.net/ by accessing “FEEs” on your personal area, select the C-HPP Satellite Workshop and save.

Location: Forum Dom Pedro Vilamoura Main Conference Hall

Date: Friday May 13, 2022 Time: 14:00 – 17:00

Agenda:

Welcome by Chris Overall, Chair C-HPP 14:00-14:05
Lydie Lane, Co-Chair C-HPP, Chair Chromosome 2 Team: "Update on Progress in Completing the Human Proteome, neXtprot Release 2022" (20 + 5 minutes)" 14:05-14:30
Gong Zhang, Chair Chromosome 8 C-HPP Team: "The discovery, function and evolution of the hidden human proteome translated from "non-coding RNAs" (20 + 5 minutes) 14:30-14:55
Marina Gay: "How Top-down Proteomics Can Contribute to the HPP" (20 + 5 minutes) 14:55-15:20
Charles Pineau: "The HPP Grand Challenge" (20 + 5 minutes) 15:20-15:45
75 minutes Open Discussion and Goal Setting, Chairs Chris Overall and Charles Pineau including the use of DIA for missing proteins with Ulrich auf dem Keller, Chair Chromosome 21, 15:45-17:00
Meeting Close 17:00
Refreshments and dinner at a local restaurant, at own expense.

The conference hotel and nearby hotels have special rates for ProteoVilamoura participants. You must make your reservation directly with the hotels with the reservations codes listed here: https://proteo-vilamoura.sci-meet.net/travel-accommodation

The Early Career Researcher Initiative Welcomes New Members

Fri, 01 Apr 2022 21:53:32 GMT

The ECR is delighted to welcome several new members from all over the world. They will play key organizing roles in ECR activities such as mentoring sessions, networking hours, online panel discussions, competitions and more.

Dr. Sayantani Chatterjee is a Post-Doctoral Associate in Prof. Joseph Zaia’s research group in Boston University School of Medicine in Boston, Massachusetts, USA. Her current research focuses on exploring viral glycoproteomics, particularly of influenza and SARS-CoV-2 viruses, using high-throughput mass spectrometry, to aid in the development of effective therapeutics. Previously, she completed her PhD under the supervision of Dr. Morten Thaysen-Andersen from Macquarie University, Sydney, Australia where she investigated the structure, function, and involvement of mannose-terminating glycoproteins in cancer, innate immunity and pathogenic infections.

Ireshyn Govender is a senior researcher in the Molecular Diagnostics and Omics group at the Council for Scientific and Industrial Research (CSIR), South Africa. He started his career at CSIR in 2013 as a candidate researcher, where his research focused on clinical proteomics in HIV/AIDS-based precision medicine. His Ph.D. was completed in 2019 at the University of the Witwatersrand. Ireshyn is also an application specialist at ReSyn Biosciences where he develops novel sample preparation workflows for biofluid-based clinical proteomics. He is a member of clinical research groups that use proteomics to address diseases that are prominent in South Africa and underrepresented populations by identifying prognostic and/or diagnostic protein biomarker panels. He is also an executive committee member of the South African Association for Mass Spectrometry (SAAMS).

Charlotte Hutchings is a PhD student in Kathryn Lilley's laboratory at the University of Cambridge. Having completed her BSc and MSc at Imperial College London, Charlotte's primary interest lies in the optimization of gene therapy vectors. It was this interest that led Charlotte to enter the world of proteomics where she now applies novel spatial proteomics methods to understand the mechanism by which adeno-associated viral vectors (used in approved gene therapies) are secreted from HEK293 producing cells. The aim of this work is to optimize the manufacturing of such vectors in collaboration with AstraZeneca. Outside of her project, Charlotte participates in public outreach events and acts as a STEM Ambassador for the North East region of England. She is also a member of the British Society for Proteome Research and the Biochemical Society and is continuing to expand her network.

Santosh Misal is a Proteomics Scientist at the Laboratory of Malaria, Immunology, and vaccinology (LMIV), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda MD, USA. He manages a small proteomics facility and provides support to the LMIV investigators for the malaria biomarker discovery and vaccine development pipeline. He utilizes various proteomics approaches including chemical labeling, crosslinking, and single-cell protein analysis to identify parasite protein targets for vaccine development. Before joining NIH, he was a postdoctoral scientist at Brigham Young University and Indiana University Bloomington. Santosh obtained his Ph.D. degree in Biochemistry from Savitribai Phule Pune University, India with a strong interest in protein analysis.

Sri Ramarathinam has over 15 years of cumulative experience in proteomics and immunopeptidomics. After completing Master of Biotechnology from RMIT University, he worked as a Research Assistant at the University of Melbourne for four years in proteomics, before completing PhD in HIV immunobiology from Monash University. He is currently working as a post-doctoral research fellow at the immunopeptidomics lab headed by Prof Tony Purcell at Biomedicine Discovery Institute (Monash). His research interests include development of new methodologies to address questions in virology, antigen processing and presentation, cancer and autoimmunity. He is also passionate about ECR well-being and is part of institute- and faculty-level ECR committees.

HUPOST March 2022

Wed, 02 Mar 2022 20:06:02 GMT

March issue of the HUPOST is now available. Lots of updates to check out!

HUPOST February 2022

Fri, 04 Feb 2022 04:10:40 GMT

Catch up on HUPO news with the February HUPOST!

The HUPO Early Career Researcher Initiative welcomes two new members!

Wed, 02 Feb 2022 05:57:19 GMT

The HUPO ECR Initiative is excited to welcome two new members to its organization: Jessica Del Castillo Alferez, a Ph.D. candidate at the University of Utrecht in the Netherlands, and Isabell Bludau, a postdoctoral fellow at the Max Planck Institute in Germany. Learn more about these two up-and-coming researchers below.

Jessica Del Castillo Alferez is a Ph.D. candidate at Sanquin Research Amsterdam and the University of Utrecht, Netherlands. Her research focuses on the development of plasma peptidomics and proteomics approaches to unravel fundamental aspects of haemostasis. She obtained her bachelor’s degree in Biochemistry at UDLAP, Mexico with a one-year exchange at McGill University, Canada. After this, she moved to the Netherlands where she completed a Master’s program in Molecular Medicine at the University of Groningen. During her Master’s internship, she entered the field of clinical proteomics while investigating proteomic adaptations of asymptomatic MCADD. Jessica is part of the Symphony Consortium, which aims to improve treatment for bleeding disorders by addressing interindividual variation in bleeding tendency. As part of Symphony, her Ph.D. project seeks to link the proteome to the bleeding phenotype with the use of plasma and blood cell profiles to study modifiers of haemostasis.

Isabell Bludau is a postdoctoral fellow in the lab of Prof. Matthias Mann, at the Max Planck Institute of Biochemistry near Munich. She is specialized in computational proteomics and systems biology. During her Ph.D. with Prof. Ruedi Aebersold at ETH Zurich, Isabell developed computational methods for analyzing large-scale proteomics data. She specifically worked on the detection and quantification of protein complexes. Recently, Isabell’s work focused on the inference of proteoforms and their crosstalk. Isabell’s PhD thesis was awarded the ETH silver medal and her postdoctoral research is supported by a Postdoctoral Mobility fellowship of the Swiss National Science Foundation. Since 2020, Isabell is a member of the organizing committee of the ISCB’s Community of Special Interest (COSI) on Computational Mass Spectrometry (CompMS), which organizes conference sessions and aims to build a community of scientists working in CompMS.

November 2021 HUPOST

(Past member) — Wed, 03 Nov 2021 17:15:36 GMT

Catchup on the latest HUPO updates in the November HUPOST:

https://conta.cc/3CI9vv5

We Are 20!

(Past member) — Wed, 03 Nov 2021 17:10:01 GMT

Founded in 2001, HUPO turned 20 this year! We are celebrating 20 years of excellent scientific conferences, community engagement, science advocacy, and advanced education! The annual HUPO world congress has been a key event for proteomics scientists since 2002, and has continued through financial and recent pandemic challenges to this year. HUPO community-centric projects, from the Human Plasma Proteome Project of 2001 to the HPP Grand Challenges of today provide cristallisation points for intensive global collaborations, advancing proteomics science and networking. Strong engagement of early career researchers is culminating in five ECR-organised sessions and five days of online training at this year's HUPO ReCONNECT!

For an interactive look through the intertwined history of HUPO and proteomics, check out https://www.hupo.org/Proteomics-Timeline, for a look at the future of proteomics attend our week-long birthday party, the HUPO ReCONNECT congress at https://hupo2021.org/. We're looking forward to virtually meeting you at www.hupo2021.org!

The Young Proteomics Investigators Club (EuPA) is Hosting a Free Webinar

(Past member) — Mon, 01 Nov 2021 20:09:59 GMT

Participate in the upcoming YPIC webinar “From Proteomics to Careeromics” on Wednesday December 8 at 11 AM CET (10 AM UTC) with Sarah Blackford (MA, Warwick University). As with proteomics (but not as technically complex or advanced!), careers are made of a multitude of facets that, when considered together, start to form a bigger picture. In this webinar, we will look at these aspects individually and together with the aim of harnessing this knowledge to reveal future career possibilities. With examples related to the interests of ECRs, the session will draw on conceptual and practical applications that should help you to make informed career decisions and take action. As always participation is free of charge! To join, register through this link: https://us06web.zoom.us/meeting/register/tZIuf-GrpzgjGNQ0iFYdrbIPDrfRS0mcHLDy

Join us at the HUPO ReCONNECT 2021 ECR Virtual Lounge

(Past member) — Mon, 01 Nov 2021 19:56:36 GMT

HUPO ECR will have a virtual lounge in Gather.Town during HUPO ReCONNECT 2021! Come join us to have a chat, relax, play games, or learn more about ECR activities. Also, you may even get the opportunity to network with some of our surprise guest scientists!!! Keep an eye out for more announcements! HUPO ECR Initiative members will also be at the lounge during conference breaks. This will be THE place to hang out during HUPO ReCONNECT 2021!

The HUPO ReCONNECT 2021 ECR Networking Hour is a Can’t-Miss Event on November 16th, 2021, at 21:15 (UTC)!

(Past member) — Mon, 01 Nov 2021 19:52:36 GMT

Join us for an opportunity to meet fellow junior researchers and mentors from around the globe! The ECR Networking Hour will be the perfect time to foster new connections for future collaborations and jobs. To take full advantage of the session, we strongly encourage all participants to keep their cameras on and participate in the light icebreaker and proteomics-related activities. Are you social media savvy or looking to get started? Keep the engagement going beyond the conference by connecting on Twitter and LinkedIn! We can’t wait to meet you!

Tune in for the Presentations of the 2021 HUPO ECR Manuscript Competition

(Past member) — Mon, 01 Nov 2021 19:42:11 GMT

The HUPO Early Career Researcher (ECR) Manuscript Competition, sponsored by Taylor & Francis, was fierce! Our three finalists, Dr. Yangsheng Liu (Yale University, USA), Dr. Stacey Malaker (Yale University, USA), and Dr. Mehdi Bouhaddou (University of California, San Francisco, USA), will be presenting their research in a dedicated session at HUPO ReCONNECT 2021 on November 17th, 2021, at 23:00 (UTC), where the final awards will be decided. A cash prize of $1,000 will be awarded to first place and prizes of $500 will be awarded to second and third. You absolutely will not want to miss these presentations!

Congratulations to the Eight Finalists of the HUPO ReCONNECT 2021 Graduate Student Poster Competition!

(Past member) — Mon, 01 Nov 2021 19:28:52 GMT

Thank you to all of the graduate students who participated in the HUPO ReCONNECT 2021 Graduate Student Poster Competition, sponsored by Molecular Omics. The evaluation committee was very impressed by the caliber of the submitted abstracts! We would like to extend a huge congratulations to the eight finalists of the competition, who will be presenting a short talk during a dedicated session at HUPO ReCONNECT 2021 (November 15th, 20:00 UTC):

Kruttika Dabke, Cedars Sinai Medical Center
Soroush Shahryari Fard, University of Ottawa
Carlos López Gil, Vall Hebron Institut Recerca (VHIR)
Fynn Hansen, Max Planck Institute for Biochemistry
Emily Hashimoto-Roth, University of Ottawa
Christin Kappert, MPI of Experimental Medicine
Sandeep Kaur, University of South Wales
Linda Berg Luecke, Medical College of Wisconsin

An expert committee will declare a winner ($300 prize) and two runner ups ($150 prizes). Good luck to all our finalists!

The HUPO ReCONNECT 2021 ECR Mentoring Sessions are Ready to Roll!

(Past member) — Mon, 01 Nov 2021 19:15:15 GMT

Three ECR Mentoring Sessions are taking place during HUPO ReCONNECT 2021, and you will not want to miss a single one. Each session will be covering an important topic, answering a slurry of questions from trainees and early career researchers. There to answer your questions will be panels of distinguished and experienced mentors – we can’t wait to see you there!

How to successfully balance a personal life while in academia (November 15th, 2021, 16:00 UTC)

Dr. Christine Carapito, University of Strasbourg
Dr. Harry Whitwell, Imperial College London
Dr. Jennifer Geddes-McAlister, University of Guelph

Scientific Integrity (November 17th, 2021, 20:00 UTC)

Dr. Stephen Pennington, University College Dublin
Dr. Suzanne Farley, Editorial Director at PLOS
Dr. Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute

Getting started on writing manuscripts, grants, and fellowships (November 19th, 2021, 4:30 UTC)

Dr. Yasushi Ishihama, Kyoto University
Dr. Rebekah L. Gundry, University of Nebraska
A representative from Molecular Omics

Congratulations to the nine HUPO members named on the Analytical Scientist’s 2021 Power List!

(Past member) — Mon, 01 Nov 2021 18:03:19 GMT

The Power List is a celebration of influential analytical scientists, and the 2021 Power List is particularly exciting, as it coincides with the Analytical Scientist’s 100th issue. HUPO is so proud that not one, but nine of its members made this year’s list. Congratulations to you all!

Dr. Jennifer Van Eyk
Dr. John Yates
Dr. Joseph Loo
Dr. Lingjun Li
Dr. Matthias Mann
Dr. Renã Robinson
Dr. Richard Smith
Dr. Ruedi Aebersold
Dr. Ying Ge

To view the complete 2021 Power List, click here!

It’s Not Too Late to Register - HUPO 2021 ReCONNECT

(Past member) — Mon, 01 Nov 2021 16:37:56 GMT

HUPO 2021 ReCONNECT starts in just a few days with the Pre-Congress program (November 8 – 12) followed by an exciting Main Congress Program (November 15 – 19). Included in your registration are not only attendance during the live days but also access to the recordings for all sessions until February 28, 2022.

Pre-Congress Program (November 8 – 12)

Pre-Congress Training Courses: Highly engaging introductory level Proteomics Fundamentals Training Courses for students and researchers. You must watch the pre-recorded presentations in advance as the Live Day sessions will focus on live Q&A with the speakers. For more information: https://hupo2021.org/pre-congress-training-courses/
HPP Sessions: Receive updates and engage in interactive discussions on the future of the HUPO Human Proteome Project (HPP). For more information: https://hupo2021.org/hpp-day/
Bioinformatics Hub: The Bioinformatics Hub is a place where bioinformaticians gather together to exchange knowledge, discuss current issues and challenges in proteomics informatics and to work on interesting, synergistic projects. For more details: https://hupo2021.org/bioinformatics-hub/

Main Congress Program (November 15 – 19)

Plenary, Keynote and Abstract Sessions: Join us for presentations from world renowned speakers and abstract presenters discussing the latest research and development in proteome research.
Hot Topic Discussions: These highly interactive and engaging discussions will cover trending, in-demand topics featuring subject matter expert panelists and moderators. These sessions are meant to spark discussion and give delegates the opportunity to directly ask questions, share thoughts and get clarity around topics that matter most. For more information: https://hupo2021.org/hot-top-discussions/
Mentoring Sessions: Three engaging sessions will cover topics on how to successfully balance personal life while in academia, scientific integrity and how to write manuscripts, grants and fellowships.
Poster Sessions: More than 400 electronic posters will be presented and you will be able to talk directly to the presenter via video chat.
Industry Symposia (On-Demand and Live): Join our industry partners in their live and on demand sessions to learn more about their products and services.

Our Virtual Platform Is Now Open For You To Explore
Our highly interactive virtual platform Gather.Town is already open for all registered delegates to explore. During the live days you will be able to see and directly talk to other people as you ‘bump’ into them on the platform. Create your own avatar, join conversations and mingle between groups.

October 2021 HUPOST

(Past member) — Tue, 05 Oct 2021 18:20:48 GMT

Catchup on the latest HUPO updates in the October HUPOST:

https://conta.cc/3ASuoTc

Another Successful HUPO ECR Online Panel Discussion

(Past member) — Thu, 30 Sep 2021 14:18:50 GMT

In partnership with the European Proteomics Association’s Young Proteomics Investigators Club (YPIC), the HUPO ECR Initiative hosted its second online panel discussion on September 27th at 10AM EDT (2PM UTC). Our panelists, Dr. Kathryn Lilley (University of Cambridge), Dr. Tharan Srikumar (Bruker), and Dr. Lindsay Pino (Talus Bio), shared their insights on managing expectations between a supervisor and oneself, which sparked lively conversations with attendees in the audience. Thank you to everyone who attended, our panelists, and our panel chair, Andreas Hober (KTH Royal Institute of Technology)! If you missed the live webinar you can view the recording here.

The next panel will be on Choosing and Managing Collaborations: Do’s and Don’ts. Stay tuned for more details and registration information!

Good luck to All Participants of the HUPO ReCONNECT Graduate Student Poster Competition!

(Past member) — Thu, 30 Sep 2021 14:15:46 GMT

Thank you to all of those who submitted an abstract for the HUPO ReCONNECT 2021 Graduate Student Poster Competition, sponsored by Molecular Omics! We are thrilled to report that 60 Master’s and Ph.D. students have entered the running. After careful evaluations over the coming days, eight finalists will be selected and granted the opportunity to present a short talk in a dedicated session at HUPO ReCONNECT 2021 (November 15th, 20:00 UTC) and an expert committee will declare a winner ($300 prize) and two runner ups ($150 prizes). Good luck to all our participants!

2021 Council Elections

(Past member) — Thu, 30 Sep 2021 14:11:58 GMT

The election period to vote for the HUPO Council is October 18 - November 14, 2021. All active HUPO members will receive an email containing online voting instructions on October 18. The official slate of candidates can be viewed here. Please register as a member if you wish to receive a voting ballot.

2021 GAM Meeting

(Past member) — Thu, 30 Sep 2021 14:10:11 GMT

The HUPO General Assembly of Members (GAM) will take place virtually at HUPO ReCONNECT 2021. To accommodate global time zones, two online GAM sessions will be offered as follows (you do not need to attend both sessions):

GAM Session 1: Tuesday, November 16 @ 20:00-21:00 UTC (Coordinated Universal Time)
GAM Session 2: Thursday, November 18 @ 05:45-06:45 UTC (Coordinated Universal Time)

All active HUPO members will receive an email containing login details to both sessions. Members are encouraged to attend.

Join Us on October 18 for an Exciting HUPO 2021 ReCONNECT Pre-Congress Webinar!

(Past member) — Thu, 30 Sep 2021 14:02:16 GMT

Real-World Precision Medicine: Proteogenomics to Accelerate Drug Development and Patient Care (90minutes)

October 18, 2021
08:00 PDT (UTC-7), 11:00 EDT (UTC-4), 15:00 UTC

Ever since the announcement of the Precision Medicine Initiative, there have been increasing efforts to identify and understand the basis of cancer using high-throughput technologies and the development of specialized treatments for specific subtypes of cancer, based on molecular evidence. Clinical proteogenomics is an exciting opportunity to complement the gene testing-centric clinical community for precision medicine. However, translating proteomic measurements to real-world patient care requires synergy of multiple requirements: meaningful and actionable molecular characterization, clinical and analytical validation, defining diagnosis values, and meeting regulatory compliance.

Speakers:

New Nominations and Elections Committee Co-Chair - Sisi Wu

(Past member) — Wed, 29 Sep 2021 20:21:43 GMT

The Nominations and Elections Committee welcomes Sisi Wu as the new Co-chair, who will join Aleksandra Nita-Lazar in managing the activities of the NEC.

Dr. Wu received her Ph.D. from the Washington State University (James Bruce’s laboratory), developing novel methods for mass spectrometry-based proteomics. Between 2006 and 2008, she conducted her postdoctoral research on top-down proteomics at the Pacific Northwest National Laboratory (PNNL) with Drs. Ljiljiana Pasa-Tolic and Richard Smith. Later, she worked as a research scientist at Battelle Toxicology Northwest (2008-2010) and a senior scientist at PNNL (2010-2014). In 2015, Dr. Wu joined the Department of Chemistry and Biochemistry at the University of Oklahoma as an assistant professor. Sisi has nearly 20 years of experience in developing advanced top-down and bottom-up proteomics techniques to understand protein dynamics and functions in different biological systems. She is particularly interested in solving clinical and biological questions through integrating technologies in life sciences, biology, separation science, MS instrumentation, and bioinformatics. Her research program is focused on development and application of the new top-down MS and functional proteomics technologies in order to characterize intact proteins and their modified proteoforms. Sisi had been a HUPO Council member since 2019.

HUPO ReCONNECT ECR Networking Hour

(Past member) — Tue, 31 Aug 2021 21:29:25 GMT

Join us for the HUPO ReCONNECT ECR Networking Hour on November 16th, 2021 at 21:15 (UTC)!

The ECR Networking Hour is an open forum session to bridge the digital, cultural, and continental gaps so that early career researchers can meet, share, and create connections for future collaborations and support in their job search. Participants are encouraged to engage with their cameras on and join in our icebreaker and proteomics-related networking activities. In preparation for the ECR Networking Hour, participants are also encouraged to set up a LinkedIn or Twitter handle to keep the engagement going beyond November 16th!

The HUPO Early Career Researcher Initiative Welcomes New Members from Asia!

(Past member) — Tue, 31 Aug 2021 19:28:20 GMT

The HUPO Early Career Researcher Initiative is actively working on diversifying its team members to be more representative of the global proteomics community. It is with our utmost pleasure to introduce our two new members Dr. Mio Iwasaki, an Assistant Professor at Kyoto University, Japan, and Dr. Dongxue Wang, a Research Scientist at the National Center for Protein Science in Beijing, China. We look forward to their contributions moving forward! Please read more about Dr. Iwasaki and Dr. Wang below.

Mio Iwasaki is an assistant professor at the Center for iPS Cell Research and Application, Kyoto University, Japan. In March 2013, she obtained her Ph.D. in Dr. Ishihama’s lab at Kyoto University. She is now working on identifying essential post-transcriptionally regulated genes in each cell type and tissue. She is also a member of jPOST, which is the Japanese proteome database repository with a nice user interface and a quite fast data uploading system.

Dongxue Wang, is a research scientist at the National Center for Protein Science in Beijing (NCPSB), China. She was trained as a system biologist trained in mass spectrometry by Bernhard Kuster at the Technical University of Munich in Germany. After obtaining her Ph.D. in 2018, she joined NCPSB. Dongxue is developing and applying state-of-the-art proteomic methods to quantitate protein expression in tissues and bodily fluids, to better understand the human biology and diseases.

Meet the Speakers for the HUPO ReCONNECT ECR Mentoring Sessions!

(Past member) — Tue, 31 Aug 2021 18:45:06 GMT

We are so excited to announce some of the mentors that are confirmed for our ECR Mentoring Session speakers for HUPO ReCONNECT 2021. The three sessions taking place throughout the conference will cover three different topics and are shaping up to be ones to remember! Check out our roster below:

How to successfully balance a personal life while in academia (November 15th, 2021 at 16:00 UTC)

Dr. Christine Carapito, University of Strasbourg
Dr. Harry Whitwell, Imperial College London
Dr. Jennifer Geddes-McAlister, University of Guelph

Scientific Integrity (November 17th, 2021 at 20:00 UTC)

Dr. Stephen Pennington, University College Dublin
Dr. Suzanne Farley, Editorial Director at PLOS

Getting started on writing manuscripts, grants, and fellowships (November 19th, 2021 at 4:30 UTC)

Dr. Yasushi Ishihama, Kyoto University
Dr. Rebekah L. Gundry, University of Nebraska
A representative from Molecular Omics

Congratulations to Our Three HUPO ECR Manuscript Competition Finalists!

(Past member) — Tue, 31 Aug 2021 18:20:38 GMT

The HUPO Early Career Researcher (ECR) Initiative would like to extend a big thank you to everyone who entered the ECR Manuscript Competition. The competition was fierce! We would like to further congratulate our three finalists, Dr. Yangsheng Liu (Yale University, USA), Dr. Stacey Malaker (Yale University, USA), and Dr. Mehdi Bouhaddou (University of California, San Francisco, USA), who will be presenting their research in a dedicated session at HUPO ReCONNECT 2021 on November 17th at 23:00 (UTC). Learn more about our finalists below.

Dr. Yansheng Liu received his Ph.D. in Biomedical Sciences from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences in 2011. He then completed a 6.5-year post-doctoral training in the laboratory of Dr. Ruedi Aebersold at ETH Zurich, Switzerland. In December 2017, he joined the faculty at the Yale Cancer Biology Institute and the Department of Pharmacology at Yale. His research group at Yale aims to contribute to the development of multiplexed, high-throughput data-independent acquisition mass spectrometry (DIA-MS) technique and other proteomic methods, as well as their applications in protein turnover, cancer aneuploidy, and cancer signaling transduction. Dr. Liu has co-authored 55 publications with a total citation of 4,500 times. Dr. Liu has received the 2021 ASMS research award. He serves as an editorial board member of Proteomics and Proteomics-Clinical Applications, a scientific advisory board member for Review Commons, and a member of the HUPO Awards Committee.

Dr. Stacey Malaker is an Assistant Professor in the Department of Chemistry at Yale University. Her laboratory is focused on establishing methods and technology to study mucins, a class of densely O-glycosylated extracellular proteins, by MS. Additionally, the laboratory studies mucins in a biological context, since these proteins play integral, yet poorly understood, roles in numerous diseases. Prior to her appointment at Yale, she received her B.S. from the University of Michigan in Biochemistry and Anthropology-Zoology. Dr. Malaker then went on to receive her PhD in Chemistry from the University of Virginia in the laboratory of Professor Donald Hunt. She continued to investigate the role of aberrant glycosylation in cancer as an NIH postdoctoral fellow in Professor Carolyn Bertozzi’s laboratory at Stanford University before starting at Yale in 2021.

Dr. Mehdi (“Meh-Di”) Bouhaddou acquired his bachelor’s degree from the University of California, Berkeley and his PhD in Biomedical Sciences at the Mount Sinai School of Medicine. He is currently a National Cancer Institute postdoctoral fellow at the University of California, San Francisco (UCSF) advised by Dr. Nevan Krogan. Using both experimental and computational approaches, Mehdi specializes in integrating large biological datasets to understand how diseases, and potential therapies, can rewire cellular signaling. During his PhD, Mehdi developed mechanistic mathematical models of cancer signaling pathways, depicting their dynamical behavior in response to anti-cancer agents. He has since repurposed his skills in bioinformatics and molecular biology to study SARS-CoV-2 and other respiratory viruses of pandemic potential, with a specific focus on studying the functional effects of viral and host post-translational modifications (phosphorylation) that occur during infection.

Looking for Translators

(Past member) — Tue, 31 Aug 2021 17:16:12 GMT

Can you speak more than one language? Are you interested in contributing to a global effort to make proteomics more visible? Are you interested in increasing your visibility within the scientific community?

If you answered yes to any or all of these questions, HUPO Marketing and Outreach Committee (MOC) would love to hear from you.

We are looking for individuals who are willing to translate existing and new HUPO material from English to different languages, to increase the HUPO outreach and to make proteomics more visible globally. The translated material (acknowledging the name of the translator) will be utilized within existing HUPO media channels, as well as to build relationships with local (e.g. continent or country-specific) proteomics societies and other societies.

In return, this opportunity will increase your visibility within the HUPO and the wider proteomics community, and additional unforeseen benefits.

If you are interested in participating please reach out via marketing@hupo.org.

August 2021 HUPOST

(Past member) — Tue, 03 Aug 2021 17:55:16 GMT

Catchup on the latest HUPO updates in the August HUPOST:

https://conta.cc/3BUAwer

2021 HUPO Council Elections

(Past member) — Mon, 26 Jul 2021 20:11:58 GMT

The Nominations and Elections Committee presents the official slate of candidates for the 2021 HUPO Council election. We would like to thank all candidates standing for Council election for a three-year term beginning in January 2022 (2022-2024). The election period for HUPO Council is October 26 – November 16, 2021.

The list of candidates is available here. We encourage you to review the slate of candidates prior to the election opening date.

HUPO members will receive a voting email from Simply Voting on October 26^th.

Call for Self-Nominations - Executive Committee

(Past member) — Mon, 26 Jul 2021 20:06:54 GMT

Nominations are now open for HUPO Executive Committee positions. This is an opportunity to lead the future of an important scientific organization and work with an enthusiastic global team to promote and represent proteomics.

The following positions will be elected by Council vote for a two-year term and commence in January 2022:

President-Elect (2022), President (2023-2024), Past President (2025)
Vice President (2022-2023)
ECR Representative (2022-2023) - appointed by the ECR, ratified by Council

Click here to view a list of the current HUPO Executive Committee.

For information on how to apply, please click here.

The deadline to submit self-nominations is August 31, 2021.

We look forward to your participation.

In Loving Memory of Prof. Pengyuan Yang

(Past member) — Mon, 28 Jun 2021 17:49:21 GMT

Remembering a pioneering scientist, distinguished leader and our good friend on the journey to advance mass spectrometry-based proteomics

We are deeply saddened by the loss of a distinguished colleague and friend in the HUPO community, Prof. Pengyuan Yang, Executive Vice Director of the BioMedical Sciences and Principal Researcher of the Biological Mass Spectrometry Group, Fudan University, in May 31, 2021.

Pengyuan received his PhD from the department of chemistry, University of Massachusetts and worked as a post-doc in Indiana University and Xiamen University. He then joined Xiamen University and Fudan University to start his career. Throughout his life, Pengyuan has been devoted to the development of instrumentation and methodology in the fields of analytical chemistry and proteomics. Pengyuan pioneered mass spectrometry-based instrumentation and methodology when proteomics was still in its infancy. With his keen vision, he constructed the very first ESI-Q-TOF mass spectrometer in China and kept promoting the development of mass spectrometry instruments and their application in proteomics. Pengyuan has made extraordinary contributions to the development of proteomics research in China. He has led two national “973” projects aiming to develop advanced proteomics and microfluidics, starting in the historical period when scientists gradually shifted their 2D gel to mass spectrometry-based proteomics. He also led one national “863” project aiming to develop MS instrumentation and relevant reagents. He has published more than 500 articles with over 16,000 citations. In particular, he has developed a series of techniques for identification and quantification of the glycoproteome, in particular pGlyco. These “sweet” techniques and informatic tools will remain a great legacy to benefit the study of the highly complex glycobiology.

We are so grateful to have Pengyuan with his life-long contribution to HUPO. Until the last stage in his life, Pengyuan actively participated in the Human Proteome Project (HPP) under HUPO. He served as an elected council member of HUPO, and past member-at-large of the Human Proteome Project (HPP), playing key role to direct and coordinate the activities of HPP.He also was a leading member under the Human Disease Glycomics/Proteome Initiative (HGPI). Aligned with the international efforts under the chromosome-centric Human Proteome Project (C-HPP), he also lead a team to decode the protein compositions of chromosome-8 and understand the biological context of the protein parts list. PangYuan’s passion, efforts and contribution to the proteomics community are highly recognized and appreciated.

We believe that the spirit of PengYuan will live on. His legacy will be inherited by more researchers and continue to contribute to create new generations of instruments, applications of mass spectrometry and their translation into precision medicine. On behave of HUPO, we would like offer our condolences to Pengyuan's family.

Yu-Ju Chen, President
Susan E Weintraub, Vice President
Henning Hermjakob, Secretary-general
On behalf of Human Proteome Organization (HUPO)

Huali Shen, Professor
On behalf of Pengyuan Yang’s group

HUPO Proteomics Knowledge Resource now available

(Past member) — Wed, 23 Jun 2021 18:31:01 GMT

The HUPO Proteomics Knowledge Resource is now available - a virtual library where you can view posters, recordings, training courses and industry seminars from HUPO Connect 2020. Generally, selected presentations become available six months after the original presentation. The content will be available year-round and can be accessed on-demand, for free, by all HUPO members.

HUPO Connect 2020 recordings are now available:

40 recordings from the main program
6 pre-congress webinars
45 pre-congress training courses
220 posters
16 industry seminars

The content will be available year-round and can be accessed on-demand, for free, by all HUPO members. We will continuously be adding new content.

The Graduate Student Poster Competition returns for HUPO Reconnect 2021!

Fri, 28 May 2021 23:35:07 GMT

Written by Emily Hashimoto-Roth, University of Ottawa, Canada

The HUPO Early Career Researcher Initiative is excited to announce the return of its Poster Competition for HUPO Reconnect 2021. Starting this year, the competition now opens to both Master’s and Ph.D. students to maximize inclusivity. Selected posters will have the opportunity to give a short talk at HUPO Reconnect 2021 and the best presentations will be awarded cash prizes. More details will be provided shortly regarding registration to the competition.

HUPO Early Career Researcher Initiative successfully launches new interactive panel series!

Fri, 28 May 2021 23:33:29 GMT

Written by Emily Hashimoto-Roth, University of Ottawa, Canada

In partnership with the European Proteomics Association’s Young Proteomics Investigators Club (YPIC), the HUPO Early Career Researcher Initiative hosted its first online panel discussion on May 17th at 7PM EDT (GMT-4/New York Time). Our panelists, Dr. Yu-Ju Chen (Academia Sinica, Taiwan), Dr. Renã A. S. Robinson (Vanderbilt University, USA), and Dr. Robert Rivers (National Institutes of Health, USA), shared their insights on the importance of promotion of diversity in proteomics, which sparked lively conversations with attendees in the audience. Thank you to everyone who attended, our panelists, and our panel chair, Emily Hashimoto-Roth (University of Ottawa)!

Our next panel will cover managing expectations between a supervisor and oneself and be taking place in July. Stay tuned for more details and registration information!

HUPO Reconnect 2021 ECR Manuscript Competition is accepting submissions

Fri, 28 May 2021 23:31:42 GMT

Written by Emily Hashimoto-Roth, University of Ottawa, Canada

Are you an early career researcher who published, or had a paper accepted for publication, after January 1st, 2020? We highly encourage you to submit your manuscript to the ECR Manuscript Competition! Eligible early career researchers include post-doctoral fellows (Ph.D. awarded post January 2015), faculty members (appointed post January 2017, with Ph.D. awarded post January 2009), and clinicians (M.D. awarded post January 2014), all of whom must also be HUPO members. Following deliberation by a selection committee, three finalists will have the opportunity to give an oral presentation at HUPO Reconnect 2021, where awards and cash prizes will be granted – $1,000 to the winner and $500 to the two runners-up. For complete competition details and to learn how to submit your manuscript, please visit: https://hupo2021.org/ecr-manuscript-competition/. The deadline to submit is June 14th, 2021.

Cold cases: Applying quantitative proteomics to resolve rare disease diagnoses

Fri, 28 May 2021 22:54:01 GMT

Written by Daniella H. Hock, Department of Biochemistry and Pharmacology, Bio21 Institute, The University of Melbourne, Australia; David Thorburn, Murdoch Children’s Research Institute, Royal Children’s Hospital, Department of Paediatrics, University of Melbourne, Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Royal Children’s Hospital, Australia; David A. Stroud, Department of Biochemistry and Pharmacology, Bio21 Institute, The University of Melbourne, Australia

Mitochondria are central to energy metabolism, producing the vast majority of cellular ATP via the oxidative phosphorylation (OXPHOS) system, while also being involved in other important processes such as one carbon metabolism, calcium homeostasis, and Fe-S cluster biogenesis (1, 2). Mitochondria are fascinating organelles as they possess their own circular DNA (mtDNA) which encodes 13 proteins translated via their own ribosomes (mitoribosome) while the remaining proteins are translated in the cytosol and imported into the mitochondria (3).

Mitochondrial disease is an umbrella term for a collection of rare genetic disorders where cells fail to produce enough energy for proper organ and tissue function (2, 4). Collectively, it affects at least 1 in 5,000 live births (5) with infants affected by the disease having a particularly poor prognosis. From the over 1,100 known proteins localised to the human mitochondria (6), at least 350 are encoded by genes in which mutations are known to cause mitochondrial disease (4). Mitochondrial disease displays extreme clinical and genetic heterogeneity, can develop at any stage of life, and usually affects organs with high energy demand such as brain, heart, liver and skeletal muscle (2, 4).

Once mitochondrial disease is suspected based on clinical investigation, the search for the genetic variant starts (Fig. 1A). The current diagnostic paradigm typically involves massively parallel sequencing (MPS) approaches such as whole-exome sequencing (WES) and whole-genome sequencing (WGS). Despite these combined approaches, the diagnosis of mitochondrial disease is only achieved in 35-60% of suspected cases and often after years of investigation (7). For some unsolved cases, more than one variant of uncertain significance (VUS) is flagged following bioinformatic analysis, potentially requiring further functional validation to confirm pathogenicity e.g., spectrophotometric assays of OXPHOS enzyme activity and western blot analysis of single proteins. Alternatively a single pathogenic variant is found in a gene associated with autosomal recessive inheritance and it can be unclear if a second “cryptic variant” has been missed. More recently high throughput omic approaches, such as transcriptomics and proteomics, have begun to be integrated into investigations of variant pathogenicity (8). The ‘unbiased’ nature of these techniques also lends themselves to gene discovery in cases where no candidate VUS are identified. The integration of multi-omic approaches into the diagnosis of mitochondrial disease is thus not only decreasing the waiting time for a diagnosis but potentially allowing an earlier use of therapies, disease management and facilitating provision of information that can inform family planning decisions.

Since 2017 we have been developing and applying quantitative proteomics approaches to undiagnosed cases of rare diseases with a focus on patients with clinically suspected mitochondrial disease, while also investigating genes that can potentially cause mitochondrial diseases (9). We have analysed a range of primary tissues, including fibroblasts from skin biopsies, lymphoblasts from blood, myoblasts, skeletal muscle and heart biopsies, and have tested different quantitative approaches to individually address each clinical case. At its most basic, we have applied label free quantitative analysis of proteome changes in whole patient material relative to a panel (usually 3-5) of controls (Fig. 1B). We have also employed fractionation of peptides for increased proteome depth, pulse labelling with stable isotopes to monitor mtDNA translation, isobaric labelling, and other approaches. Our efforts have supported the published (10-13) and unpublished diagnosis of over 30 patients, many of whom were undiagnosed for decades after extensive investigation, thus demonstrating that quantitative proteomics is a technique capable of providing evidence to support disease causation arising from various types of variants, including deep intronic variants, splice site variants, copy number variants, and missense variants present in either mitochondrial or nuclear DNA.

The first cold case we would like to share had been undiagnosed for over 10 years, despite inconclusive results after extensive investigations which included [i] chromosomal microarray and breakage analysis, [ii] quad (both parents and affected siblings) whole exome sequencing, [iii] common mitochondrial DNA point mutations, [iv] and the gold-standard quad whole genome sequencing (11). Transcriptomic analysis (RNA sequencing) was performed and identified a reduction in NDUFB10 expression as well as novel splicing events, including the presence of a cryptic exon in NDUFB10 transcripts (Fig. 1C). We performed label free quantitative proteomics on skin fibroblasts from the patient and three control individuals. NDUFB10 peptides were actually not detected in control or patient cells but we confirmed the reduction in over twenty NDUFB10 partner proteins in patient cells, similar to the protein signature observed in knockout NDUFB10 cells (14). These proteins, along with NDUFB10 are subunits of the first complex in the mitochondrial respiratory chain, also called Complex I or NADH ubiquinone oxidoreductase. The abundance of subunits in the other complexes of the OXPHOS system were unaffected. Reanalysis of WGS data confirmed the presence of a novel deep intronic cryptic splicing variant in NDUFB10, found in homozygosity in the affected siblings and in heterozygosity in the parents.

The second investigation involves the diagnosis of 17 patients where inherited deletions and de novo duplication had occurred in the repetitive ATAD3 locus. Mutations in this locus are now known to be one of the five most common causes of paediatric nuclear-encoded mitochondrial disease (12). The ATAD3 locus is comprised of three highly homologous genes in tandem: ATAD3C, ATAD3B and ATAD3A, an arrangement which is exclusive to hominids. The homology of the region makes it prone to nonallelic homologous recombination (NAHR) events, giving rise to copy number variations (CNVs) such as deletions and duplications. Identification of deletions and duplications events in highly homologous genomic regions can be a challenge as these regions can be refractory to the short read sequencing approaches used in WES and WGS methodologies. To overcome this problem, short read approaches were combined with long-read sequencing, transcriptomics and quantitative proteomics analyses to identify recessive biallelic deletions and dominant de novo duplications in the ATAD3 locus (Fig.1D). At the protein level, the recessive biallelic deletions give rise to a fused ATAD3B/ATAD3A protein, while the dominant de novo duplication give rise to a chimeric ATAD3A/ATAD3C protein.

Quantitative proteomics was shown to provide valuable functional data that can add to the body of evidence needed to confirm pathogenicity of VUS in rare and long-term undiagnosed cases. Our current efforts are now focused on developing a high throughput and robust quantitative proteomics pipeline to be incorporated into routine clinical investigations of patients with suspected but undiagnosed rare disease in order to decrease the current diagnostic gap.

Figure 1A. Example pipeline for investigation of clinically suspected rare disease. Genomic sequencing is the first line approach followed by functional validation of variants of uncertain significance (VUS) using e.g. enzymology, western blot, transcriptomics and proteomics. B. General schematic depicting workflow for functional validation of VUS via quantitative proteomics. C. Multi-omic investigation used to identify a deep intronic variant in NDUFB10, a structural subunit of mitochondrial Complex I (CI). Transcriptomic analysis identified a cryptic exon inserted between exon 1 and exon 2 of NDUFB10. Proteomics on the patient skin fibroblasts show an isolated decrease in CI. Differential protein abundances were topographically mapped to the CI structure (PDB ID: 5LDW) for visualization of the impact of mutation. Data plotted from supplemental material in (11). D. Pathogenic genetic arrangements in the ATAD3 locus identified in patients with a large deletion or duplication in the repetitive ATAD3 locus. Deep peptide fractionation and label free quantitative proteomics of patient skin fibroblasts revealed the corresponding decrease and increase in peptide abundance. Data plotted from supplemental material in (12).

References

1. Jackson TD, Hock DH, Fujihara KM, Palmer CS, Frazier AE, Low YC, et al. The TIM22 complex mediates the import of sideroflexins and is required for efficient mitochondrial one-carbon metabolism. Mol Biol Cell. 2021;32(6):475-91.

2. Frazier AE, Thorburn DR, Compton AG. Mitochondrial energy generation disorders: genes, mechanisms, and clues to pathology. J Biol Chem. 2019;294(14):5386-95.

3. Kang Y, Fielden LF, Stojanovski D. Mitochondrial protein transport in health and disease. Semin Cell Dev Biol. 2018;76:142-53.

4. Hock DH, Robinson DRL, Stroud DA. Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome. Biochem J. 2020;477(21):4085-132.

5. Skladal D, Halliday J, Thorburn DR. Minimum birth prevalence of mitochondrial respiratory chain disorders in children. Brain. 2003;126(Pt 8):1905-12.

6. Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, et al. MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res. 2021;49(D1):D1541-D7.

7. Stenton SL, Prokisch H. Genetics of mitochondrial diseases: Identifying mutations to help diagnosis. EBioMedicine. 2020;56:102784.

8. Alston CL, Stenton SL, Hudson G, Prokisch H, Taylor RW. The genetics of mitochondrial disease: dissecting mitochondrial pathology using multi-omic pipelines. J Pathol. 2021.

9. Hock DH, Reljic B, Ang CS, Muellner-Wong L, Mountford HS, Compton AG, et al. HIGD2A is required for assembly of the COX3 module of human mitochondrial complex IV. Mol Cell Proteomics. 2020.

10. Lake NJ, Webb BD, Stroud DA, Richman TR, Ruzzenente B, Compton AG, et al. Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome. Am J Hum Genet. 2017;101(2):239-54.

11. Helman G, Compton AG, Hock DH, Walkiewicz M, Brett GR, Pais L, et al. Multiomic analysis elucidates Complex I deficiency caused by a deep intronic variant in NDUFB10. Hum Mutat. 2021;42(1):19-24.

12. Frazier AE, Compton AG, Kishita Y, Hock DH, Welch AE, Amarasekera SSC, et al. Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus. Med (N Y). 2021;2(1):49-73.

13. Van Bergen NJ, Ahmed SM, Collins F, Cowley M, Vetro A, Dale RC, et al. Mutations in the exocyst component EXOC2 cause severe defects in human brain development. J Exp Med. 2020;217(10).

14. Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, et al. Accessory subunits are integral for assembly and function of human mitochondrial complex I. Nature. 2016;538(7623):123-6.

Biography

Daniella Hock is a PhD candidate in Dr David Stroud’s lab at the University of Melbourne in Australia, where she has been developing and applying quantitative proteomics approaches to improve the diagnostic rates of rare diseases, particularly paediatric mitochondrial disease. She is also interested in investigating the molecular function of genes implicated in mitochondrial disease pathogenesis with a view toward expanding the list of genes that can potentially cause mitochondrial disease. Prior to commencing her PhD, Daniella graduated as Bachelor of Biological Sciences from Universidade Federal de Santa Catarina in Brazil and worked as molecular diagnostic scientist at Biogenetika, a personalised medicine centre, in Brazil.

The Promise of Diversity and the HUPO Vision

Fri, 28 May 2021 22:48:20 GMT

Written by Aleksandra Nita-Lazar, National Insitute of Allergy and Infectious Diseases, USA

The diversity concept is being widely applied and more and more often globally recognized – and HUPO is no exception. For a long time, HUPO has been committed to the principles of diversity, and this commitment is reflected in our membership and leadership. Welcoming differences, equal opportunity, diversity, and inclusion is not only a matter of civility, but a real benefit for any creative effort. Diversity has been long known as a biological force driving functional ecosystems, and genetic diversity in any population ensures biological success. More recently, diversity has been recognized and published in numerous reports and books reviewing the relevant research (to name a few excellent examples: ”Creativity and Problem Solving” by Scott Page; “Accuracy in Decision-making” by Katherine Phillips” and “Willful Blindness” and other books by Margaret Heffernan), demonstrating that any diverse group will always do better than a uniform one, bringing unique perspectives and abilities, fostering discovery, boosting innovation and preventing decision bias. Each individual brings unique capabilities, experiences, and characteristics, their own vision, igniting creativity and fueling resourcefulness. To gain access to the best ideas we need to create an environment where people feel supported, heard, and free to achieve their best and contribute to their full potential. The synergy of diverse teams is real.

At HUPO we are connected by a common interest in all aspects of proteome research; bringing our individual experiences will strengthen the organization further, so we intentionally cultivate diversity and inclusion. The members of HUPO represent scientists from all regions and levels – we have 48% student and Postdoc members and 38% of HUPO members are women. All the active members are eligible for election to the HUPO Council. The Nominations and Elections Committee (NEC) monitors and approves the nomination and election process. Two years ago, the requirement of 10 or more years of professional experience for eligibility was waived and now trainees and junior scientists are eligible and encouraged to be nominated. To promote diversity and reduce the dominance of well-known senior scientists in HUPO elections, each of the three regions (Eastern, Central and Western) has the authority to nominate two diversity candidates for each election, and these candidates are not directly voted on, but approved or not by the voting members. At present, 31% of the Council are the diversity delegates.

The NEC is currently looking for a new co-chair committed to improving the diversity within the HUPO leadership. HUPO members interested in this position and in making their vision and ideas a reality are encouraged to apply! Contact office@hupo.org.

Join the B/D-HPP on April 26 at PTMs in Human Disease Webinar

Tue, 20 Apr 2021 19:24:31 GMT

Connect with leaders of the Biology/Disease-Driven Human Proteome Project (B/D-HPP) at their first PTMs in Human Disease webinar focused on showcasing approaches to investigate post-translational modifications (PTMs). This webinar will consist of seven (7) presentations and a panel discussion among speakers and participants.

See list of speakers and presentation topics here: Webinar Flyer

Date: Monday, April 26, 2021

Time: 0600 PST; 0900 EST; 1300 UTC (Three (3) hours) Find your local time zone

Zoom meeting link: https://princeton.zoom.us/j/99080442592

PROTEOMICS WORKSHOP IITB-DST (15th – 26th Feb 2021)

Tue, 30 Mar 2021 23:16:03 GMT

Sanjeeva Srivastava, IIT Bombay, India

The flourishing field of advanced multi-omics technologies opened new avenues for understanding health and disease biology, specifically identifying disease-specific biomarkers and developing potential therapies. Among all multi-omics technologies, Proteomics has time and again proved vital to provide insight into disease pathology. The workflow of designing a proteomics experiment and making sense out of that data is always challenging, especially for beginners in the field.

To aid these scientists and students, Prof. Sanjeeva Srivastava from IIT Bombay, in collaboration with DST, India, organized a two weeks’ workshop on ‘Basics and Advanced Proteomics Approaches Workshop’ from 15th to 26th February 2021 to spread the knowledge in high throughput proteomics technologies and the data analysis strategies using advanced software like- MaxQuant, Proteome Discoverer, MetaboAnalyst and Reactome.

This event was a success due to the eminent scientists and experts from the industry from India and Abroad who shared their research experience, knowledge, and expertise in that field. In addition to that, Participants, mainly faculties from different universities/ institutions of India, made the workshop more interactive rather than lecture series. All participants were provided some group projects to make them more confident in data analysis and to build collaboration between them in the near future.

The first week of the workshop was conducted to enlighten the participants’ knowledge in MS-based proteomics, various approaches of quantitative proteomics like- gel-free and gel-based proteomics, and acquaint them with software for primary proteomic data analysis. In the morning sessions, plenary speakers including Prof. Marc Wilkins, Matthias Ulhén, Bernhard Küster, and Prof. Mark Baker, other eminent scientists including Prof. Surekha Zingde, Utpal Tatu, Mathias Wilhelm, Anthony Purcell gave an insightful talk on various aspects of proteomics and its applicability in clinical research. The afternoon sessions were designed to give the participants a hands-on experience in sample preparation for quantitative proteomics, including protein extraction and digestion, sample run in the mass spectrometer, monitoring of sample run, and primary and secondary analysis of proteomics data. The second week of the workshop was designed to introduce participants to the high throughput proteomics technologies like targeted proteomics, label-free biosensors like SPR, BLI, protein microarray, and network analysis to infer the biological significance from the MS data. In this week, participants got the opportunity to hear from esteemed scientists and researchers in the proteomics field Prof. Xiaobo Yu, Prof. Henning Hermjakob, Dr. Jau-song Yu, Dr. Suman Thakur. This week was more enriched with tech-talks; Mr. Michael Johnson, Dr. Rodrigo Barderas, Dr. Tian-Hua Wang, Dr. Debadeep Bhattacharyya shared their research work and the developed techniques to elevate the proteomic research. The major attraction of the second week was the group project which made participants more familiar with handling the mass spectrometric data.

Nowadays, it has become essential to upgrade us with current trends and advances in proteomics technologies to facilitate the translation of lab research to clinics. Herewith, this two weeks long workshop gave the participants an insight to use these high-throughput proteomics technologies for the progression of the clinical research.

All the workshop recordings are available at Proteomics Workshop YouTube video playlist link: https://youtube.com/playlist?list=PLIaqGH0Iwt3h01pDpyAvyJe_9PIxE1f2I

Upcoming B/D-HPP Webinar

Thu, 25 Mar 2021 23:19:55 GMT

The HUPO B/D-HPP Executive Committee is excited to announce an upcoming human proteome webinar organized by B/D-HPP in April/May 2021! The webinar will be the start of a series of online events to highlight recent progresses in proteome research from leading investigators around the globe.

The theme of the first webinar will be "PTMs in Human Disease". This 3-hour event will feature talks from ~5 to 7 leading experts on proteomics approach toward multiple types of common and rare post-translational modifications in the human proteome. More information including speaker list, title, webinar time and weblink will be posted in the coming weeks. Please stay tuned!

PROTEOMICS PERSPECTIVE - GLIMPSES (PART-I)

Wed, 03 Mar 2021 00:44:26 GMT

Did you know HUPO has a YouTube channel? From the 2017 world congress welcome address by former 47^th Vice President of the United States Joseph R. Biden Jr., to a series of interviews on perspectives in proteomics, check out videos recorded at our past congresses on YouTube.

PROTEOMICS PERSPECTIVE - GLIMPSES (PART-I)

An interview series of proteomics experts has been undertaken over the last several HUPO world congresses, and describe the challenges and goals of current basic and clinical research in the proteomics field. This perspective series is directed by Prof. Sanjeeva Srivastava, IIT Bombay, Mumbai.

British Society for Proteome Research (BSPR) Interact 2021

Wed, 03 Mar 2021 00:43:12 GMT

July 6-8, 2021

Abstract submission and early bird registration are now open for the British Society for Proteome Research (BSPR) Interact 2021 meeting. The conference features prominent and upcoming scientists from the UK and across the globe, presenting the latest research and methodology in the field of proteomics, as well as participating in round table discussions.

For more information, including on how to register and submit your abstract, please visit www.bspr-interact.com. To stay up to date, follow the BSPR on Twitter and Facebook @UKBspr, and join the BSPR LinkedIn group @BSPR - British Society for Proteome Research.

HUPO Connect 2020 Recordings Still Available

Wed, 03 Mar 2021 00:42:30 GMT

Did you attend HUPO Connect? Don't forget you have access to all recordings until March 31, 2021. Didn't attend HUPO Connect? On-demand recordings are still available for purchase. Learn more..

2021 Council Nominations is Opening Soon!

Wed, 03 Mar 2021 00:42:05 GMT

The Nominations and Elections Committee will be seeking candidates to serve on HUPO Council for a three-year term beginning January 2022 (2022-2024). Call for nominations will open on Thursday, March 25, 2021. Stay tuned for more updates in the weeks to come!

Call for 2021 Award Nominations - Open!

Wed, 03 Mar 2021 00:41:21 GMT

Do you know someone who has made an impact in the field of proteomics and deserves recognition for it? Nominate them for a HUPO award. Submission deadline is Friday, April 30, 2021. Click here to review the nomination requirements and submit...

February HUPOST 2021

Tue, 02 Feb 2021 01:20:17 GMT

Checkout the latest HUPOST released today: February HUPOST 2021

Farewell message from HUPO Past President, Stephen Pennington

Tue, 12 Jan 2021 23:11:27 GMT

Stephen Pennington, HUPO Past President, UCD Conway Institute, Ireland

It has been a genuine privilege and honour to have had the opportunity to serve as HUPO President for the past two years. The COVID-19 global pandemic has made the last 9-10 months very challenging for the HUPO community and leadership team (Executive Committee). Our thoughts go to those in our community who have been directly impacted and especially those who have lost loved ones.

I’m sure we are all conscious of the devastating negative health and social consequences of COVID-19. Amongst the very many negatives it is reassuring, and perhaps necessary, to hold onto some positive outcomes from the pandemic. The increase in public and professional awareness of the science of biology and virology, of diagnostic testing and vaccine development has been remarkable to witness. Proteomics has been at the front and centre of these efforts. Likewise, the importance of global collaboration and sharing of data has been in the spotlight. This is something that isn’t new to HUPO as global collaboration and data sharing has been at the heart of HUPO and its various initiatives for many years. We should all be proud of the contribution proteomics has made and continues to make to all aspects of COVID-19 research and clinical practice. It behoves us all to publicise these efforts and capitalise the increased public awareness and support for biological sciences to more generally promote the importance of the very real global impact of proteomics research. Raising the profile of proteomics and its “success stories” has been a consistent priority for the HPP and we should now be poised to progress this with renewed vigour.

HUPO is a global organisation that promotes equality and diversity. The dramatic events of 2020 highlighted the importance of making all aware of this. I am very grateful to Sue Weintraub not only for her steadfast support as Vice-President but also for carefully crafting HUPO’s diversity statement.

The HUPO Congresses are a highlight of the HUPO year and they have continued to showcase the very best of proteomics, presented by the very best of proteomics researchers at all stages of their scientific experience. In 2019, we had the opportunity to participate in a wonderful congress in Adelaide, Australia. Organising such a successful Congress takes a huge amount of effort so without naming names I’d like to thank the local organisers for hosting the superb science, the HPP day and allied events such as the ICPC and Immuno-peptidomics meetings and combining all this with a superbly enjoyable experience.

At the start of 2020 we were all excited by the prospect of another annual Congress – this time in Stockholm, Sweden. In a very timely manner and as the COVID pandemic was gripping the world the Stockholm local organising committee advised against a ‘face-to-face’ Congress. The decision was made to postpone the Stockholm meeting (to 2021) and hold a virtual Congress in 2020 – a first for HUPO. A virtual Organising Committee (vOC) was assembled and worked tirelessly with colleagues from ICS (our core professional conference organiser) to plan and deliver HUPO Connect 2020. In addition, to the regular repertoire of proteomics research, the Congress provided an opportunity to highlight the key role proteomics has played in COVID-19 research. At a personal level, the chance to participate in the vOC; witnessing the development of our early stage career researchers, and the Congress supporting the development of a library of the recorded presentations were highlights of 2020. There have been many other proteomics highlights including, but not limited to, the publication of the High-Stringency Blueprint of the Human Proteome, the publication of the annual HPP metrics paper and the celebration of 20 years of the Human Protein Atlas.

Of course, challenges (opportunities) remain for the continued development of proteomics and I’m very confident that HUPO under leadership of YuJu Chen will continue to catalyse the pace of proteomics successes. YuJu will be ably supported by the HUPO EC and, under the leadership of Rob Mortiz, the HPP EC.

Finally, I’d like to encourage all members and especially existing and newly elected HUPO Council members to get involved in HUPO’s activities. The old adage – the more you put in the more you get out – is as true now as it ever was.

Thank you all for giving me a wonderful opportunity and particularly to those who have guided and supported me in the last two years. It’s perhaps not wise to single out any individuals but here goes anyway….! I’d particularly like to thank Jenny van Eyk and Michelle Hill for their consistent and much valued wise counsel and support and Chelsea Prangnell for her support and willingness to share the benefit of her ‘HUPO experience’.

Welcome Message from HUPO President Yu-Ju Chen

Tue, 12 Jan 2021 23:03:10 GMT

Yu-Ju Chen, HUPO President, Institute of Chemistry, Academia Sinica, Taiwan

It is truly a great honor and a big responsibility to serve as the HUPO president in the coming two years. Since the past January, I have joined the HUPO EC and witnessed the great efforts from the leadership team led by Past President Steve Pennington and Vice-President Susan Weintraub. Among the many impressive HUPO achievements, perhaps most notable and quite unique to everyone is the HUPO Connect 2020 – the very first virtual congress for HUPO. The HUPO leadership together with supports from HPP, committees, council members, speakers and sponsors have jointly turned the challenges of COVID-19 outbreak into a landmark congress in the history of HUPO. Big thank you to Steve and Sue for your contribution and congratulation to the achievements made in the past two years. From my personal view, this is the uniqueness of HUPO that we have devoted and passionate colleagues to create an inclusive and energetic infrastructure for promoting proteomics activities. I am looking forward to working with you all to enjoy proteomics activities and to translate it into knowledge in biology, health and disease as well as tools to impact our life.

Despite the unexpected and devastating economic and social disruption caused by the COVID-19 outbreak, it indeed created an opportunity to demonstrate the global proteomic exploration to enhance our molecular understanding for the emerging disease and to facilitate development of new diagnostic and therapeutic strategies. Exciting researches are exemplified in the power of multidimensional data integrating proteomics with clinical data and machine-learning-based models for risk stratification of patients, construction of SARS-CoV-2 protein interaction network to reveal the pathogenesis mechanism as well as to identify targets for drug repurposing, identification of biomarkers and rapid development of high throughput diagnosis tools for the clinical trajectory of patients. In addition to continue to promote the International collaboration in infectious diseases from the HUPO initiative, I look forward to facilitate efforts in standardization of protocols and diagnosis methods and multi-nation clinical trial within the HUPO community. The example of COVID19 may also apply to other diseases to promote precision medicine for sustainable health.

The Human Proteome Project (HPP) is well recognized as the signature for HUPO’s research activities. The release of “ A High-Stringency Blueprint of the Human Proteome” in 2020 established the legacy of the first decade of the HUPO HPP in defining the constitutions of the complex proteome with 90% coverage based on stringent criteria. I would like to express my great appreciation to the HPP leadership led by Gil Omenn, Mark Baker and Robert Moritz, advisory board and many colleagues who have contributed to HPP in the past years. Looking ahead, the human proteome blueprint is definitely the foundation of future proteomics research.

Despite our many successes, there remains much to be done to demonstrate the utility of proteomics. To date, advancements of genomics have changed the face of biology and medicine. Despite the fact that proteins are the molecules to be targeted for many therapies, however, gene testing is gold standard and protein-based diagnosis is not well accepted as clinical assay yet. Stepping into the next 10 years of HPP, I believe that proteomics will take a similar path like genomics to create benefits of our life. To speed up the process, we can jointly define focused themes, reachable milestones and strategies to transform proteomics into utilizes in many aspects of life, such as clinical care, prevention medicine, precision agriculture, and food safety.　

“If you want to go fast, go alone. If you want to go far, go together”- African proverb.

This is my firm belief that joint wisdoms and collaborative efforts always inspire new ideas with success beyond the expectation of a single mind. After 20 years since the launch of HUPO in 2001, we are now stepping into the next phase of proteomics. It is time to redefine the forward-looking goals and strategic planning for HUPO to create impact to biology, health and society. I will continue the inclusive culture of HUPO and sincerely encourage our members and everyone who loves proteomics from different part of the world to work together and demonstrate the power of proteomics to impact our life in the future.

December 2020 HUPOST

Tue, 01 Dec 2020 23:09:10 GMT

Catchup on the latest HUPO updates in the December HUPOST: https://conta.cc/3oip1Wz.

HPP CALL FOR Co-CHAIR NOMINATIONS - EXTENDED to November 30

Tue, 20 Oct 2020 19:49:06 GMT

With the expanding goals of the HPP and aggressive timelines to drive the numerous initiatives under the HPP umbrella of activities, the HPP seek to engage a vibrant, well-organized, and goal-oriented proteomics researcher to the HPP Co-Chair position to support and assist the HPP Chair.

The HPP Co-Chair position is a 2-year term and will commence January 2021.

To apply, please submit a brief (<1 page) vision statement outlining why you are a suitable candidate for this position. Email vision statement to office@hupo.org before November 30, 2020.

Journal of Proteome Research Virtual Issue Celebrating the HUPO High-Stringency Inventory of Humanities Shared Human Proteome Revealed

Mon, 19 Oct 2020 20:22:18 GMT

In the midst of a pandemic, in the midst of the global effort to develop effective vaccines and anti-virals for SARS-CoV-2—yet, paradoxically, also in the midst of a surreal moment in history where the very science that can save millions is assailed if the facts and truth conflict with political mantra—we nonetheless can celebrate. Reminding us all of the importance and relevance of science, today, October 19, 2020, we celebrate the announcement of the draft human proteome in the opening talk at HUPO CONNECT by the First Chair of the Human Proteome Project (HPP), Dr Gil Omenn, with a virtual issue of the Journal of Proteome Research (https://pubs.acs.org/page/jprobs/vi/humanproteome). In the virtual issue the editors have compiled 60 of the most significant papers published in the Journal over the past decade on the human proteome project reflecting the diversity of the C-HPP and B/D-HPP teams, regions, approaches, impact and achievement.

The neXtProt database posted the landmark human proteome data release covering 90% of the human proteome on 17th January, 20201, which is now reported by the HPP Consortium in Nature Communications by Adhikari et al 20202. In the companion annual human proteome metrics paper by Gil Omenn et al 20203 reporting this year’s progress of the HPP, the underlying data is presented in depth. The metrics paper will be published in the 8th Special Issue of the Journal of Proteome Research dedicated to the HPP in December 2020, with the ASAP preprint online today leading this HPP Virtual Issue and with a commentary editorial by Chris Overall4.

The human proteome was identified by HPP global research teams and scientists from the wider scientific community and assembled by the Chromosome Centric-HPP (C-HPP) and the HPP Knowledgebase Pillar data curators from neXtProt PeptideAtlas, and MassIVE. The C-HPP was established in 2010 as the major initiative of the HPP to identify at least one protein form (proteoform) from each of the protein-encoding genes in the human genome. For the next high-fidelity compendium of the full human proteome and to develop a broader understanding of life, human conscience, and disease, proteomics needs more data, more patients, more scientists, and more doctors to understand life, individuality, personality and disease—science needs us all, but now, more than ever, humanity needs more science

1. https://www.nextprot.org/about/statistics

2. Subash Adhikari, Edouard Nice, Eric Deutsch, Lydie Lane, Gilbert Omenn, Steve Pennington, Young-ki Paik, Christopher Overall, Fernando Corrales, Ileana Cristea, Jennifer Van Eyk, Mathias Uhlen, Cecilia Lindskog, Daniel Chan, Amos Bairoch, James Waddington, Joshua Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio Nogueira, Gilberto Domont, Yves Vandenbrouck, Maggie Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc Wilkins, Jochen Schwenk, Emma Lundberg, Nuno Bandeira, György Marko-Varga, Susan Weintraub, Charles Pineau, Ulrike Kusebauch, Robert Moritz, Seong Beom Ahn, Magnas Palmblad, Michael Snyder, Ruedi Aebersold, and Mark Baker. A High-Stringency Blueprint of the Human Proteome, Nat. Communications, 2020, doi.org/10.1038/s41467-020-19045-9.

3. Omenn G. S.; Lane L.; Overall C. M.; Cristea I. M.; Corrales F. J.; Lindskog C.; Paik Y-K.; Van Eyk J. E.; Liu S.; Pennington S.; Snyder M.P.; Baker M.; Bandeira N.; Aebersold, R.; Moritz, R.L.; Deutsch EW. Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res. 2020, Sep 15. doi: 10.1021/acs.jproteome.0c00485.

4. Overall, C.M. J Proteome Res. 2020, October 19. The HUPO High-Stringency Inventory of Humanity’s Shared Human Proteome Revealed. https://pubs.acs.org/doi/full/10.1021/acs.jproteome.0c00794.

The Human Proteome Organization’s Proteome Project releases the major milestone 2020 Metrics paper of the Human Proteome with >90% of Predicted Human Proteins Now Credibly Detected

Mon, 19 Oct 2020 12:08:39 GMT

The 2020 Metrics of the HUPO Human Proteome Project (HPP) effort to credibly detect every protein of the human proteome has been released (see https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00485). This report now provides evidence for detected expression for >90% of the 19,773 predicted proteins coded in the human genome. The HPP annually reports on the progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. The 2020 metrics paper describes the credibly detected proteins (PE1 level) as well as the 4 other PE levels of protein evidence in a central repository for community sharing of these results. With the neXtProt release of 2020−01, 17,874 genes encoding proteins are classified as PE1 and having strong protein-level evidence. This PE1 level is up 180 proteins from 17,694 one year earlier and represent 90.4% of the 19,773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the “missing proteins” (MPs), was reduced by 230 from 2129 to 1899 since the previous year’s release neXtProt 2019−01. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry (MS) data for neXtProt, supplemented this year with extensive data from the MS repository MassIVE. The mass spectrometry data knowledge bases promoted 362 and 84 canonical proteins (PeptideAtlas and MassIVE respectively) in the last year to increase the credibly identified proteins. The Human Protein Atlas also released new protein detection repositories (based on antibody binding data to human proteins) for Blood, Brain, and Metabolic Atlases. The Biology and Disease-driven (B/D)-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions.

Of the remaining “missing proteins”, hydrophobic proteins account for about 40% of these and are compounded by protein sequence structures that are difficult to extract credible peptides for high-stringency identification. These missing proteins include large families or groups including GPCR, zinc finger, homeobox, keratin-associated, and coiled-coil domain proteins. We expect novel strategies for finding missing proteins, characterizing the functions of already-detected “dark” proteins, and utilizing proteogenomics in precision medicine to be fruitful in the coming years.

In addition, the Journal of Proteome Research will produce a year-end virtual Issue with dozens of high-impact papers from the 7 annual special issues of JPR from the Human Proteome Project.

The Human Proteome Organization’s Proteome Project releases the 10-year High‑Stringency Blueprint of the Human Proteome

Fri, 16 Oct 2020 14:35:52 GMT

The Human Proteome Project (HPP) releases the first Human Proteome Organization (HUPO)-endorsed, high-stringency Human Proteome Blueprint in Nature Communications (see https://www.nature.com/articles/s41467-020-19045-9). Like the draft “shotgun” Human Genome Project of the Human Genome Organization (HUGO), the HPP has now reached a significant decadal milestone of >90% completion of the Human Proteome that is referred to as the human proteome “parts-list”. This effort recognizes significant community efforts that enabled data inspection and re-analysis, culminating in a high stringency (i.e., rigorous, exacting standards for post-acquisition data processing and protein inferences made from MS spectral data) HPP knowledge base (KB). Additionally, to illustrate the many parallel historical innovations made by the scientific community that have driven proteomics advances, HUPO has created a publicly available interactive historical timeline to be released coincident with publication of this article (hupo.org/Proteomics-Timeline).

The HPP’s mission is to reanalyze and integrate community proteomics data with high-stringency processes, bringing increased granularity to our molecular understanding of the dynamic nature of the proteome, including all its modifications, and their relation to human biology and disease. This mission aligns closely with HUPO’s motto “translating the code of life”, providing crucial information that genomics per se cannot deliver. Completion of the HPP will enhance our understanding of human molecular and cellular biology, laying better foundations for diagnostic, prognostic, therapeutic and precision medicine applications.

Background:

In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), as an international endeavor to create a framework for global collaboration, data sharing and quality assurance, enhancing accurate annotation of the genome-encoded proteome. Over the last decade, the key resources of the HPP (the Human Protein Atlas, PeptideAtlas, MassIVE and neXtProt knowledge bases) have driven the development and refinement of guidelines and metrics to understand the definitive identification of any protein of the human proteome. Their high-stringency reanalysis of community data led to the current status of >90% identification completion rate of the Human Proteome. This knowledge is essential to discern the proteome’s role in health and disease. Here, on behalf of the proteomics community, we report the inaugural high-stringency human proteome project blueprint, illustrating roles in the diagnosis and treatment of cancers, cardiovascular and infectious disease pathologies.

Stanford scientists generate a global map of protein expression which helps explain the basis of many genetic diseases

Tue, 29 Sep 2020 21:33:12 GMT

By Erika Hunting, Stanford University, USA

Researchers demonstrate how understanding protein levels can provide insights into regulation, secretome, metabolism, and human disease.

Unraveling the genetic basis of many human diseases is a daunting task. However, understanding where the products of disease-related genes act can provide clues into disease formation. Presently, scientists examine the RNA -- the first product of a gene -- to infer the tissue where genes act. Unfortunately, there is a downfall to this method: the level of protein -- the active end product of a gene -- often correlates poorly with RNA levels. Thus, generating a map of proteins may be a more revealing approach to understanding the cardinal foundation of disease development.

In a paper published on Sept. 11 in Cell, researchers in the lab of Michael Snyder, Stanford B. Ascherman Professor and Chair of Genetics and Director of Genomics and Personalized Medicine at Stanford University School of Medicine, generated the most comprehensive protein map to date. The map shows where proteins are expressed throughout the human body,providing new insights into regulation, secretome, metabolism, and human diseases. The researchers measured relative protein levels from over 12,000 genes across 32 normal human tissues. Tissue-specific proteins were identified and compared to RNA data. Information from tissue-specific proteins could lead to novel explanations of disease phenotype that could not have been deduced by RNA information alone.

"The tissue-specific distribution of proteins can provide an in-depth view of complex biological processes that require the interplay of multiple organs,” said lead author Lihua Jiang, a proteomics expert in the Snyder Laboratory responsible for proteomics profiling of host samples of the project. “Analysis of enzymes involved in amino acid metabolism revealed different roles of each organ as well as novel organs (heart, stomach, pancreas) that are important for metabolic control. We envision this kind of analysis can shed light on the understanding of many biological processes.”

Correlation between RNA and Protein Levels

Previous studies of protein levels have already been performed. However, most of these studies focused on in-depth protein identification and analysis, and the protein measurements were either less accurate or less precise. Moreover, most samples in these studies did not have the corresponding RNA information from the same tissue, making the comparison of RNA and protein levels difficult. Although recent studies have greatly advanced tissue-protein identification, a broader study with accurate measurements for both protein and RNA levels within the same tissues is needed to understand protein level differences from RNA. Additionally, no previous studies have used tissue-specific protein data to systematically examine human biological processes and diseases.

This Snyder Lab study offered a good opportunity to characterize the correlation between protein and RNA, as data were generated from the same tissue specimens. For many genes, the Stanford team found that only the RNA (not their corresponding proteins) were present at a significant level, while for other genes, it was the opposite -- the protein was detected and not the RNA. These results indicate that tissue-specific functions cannot be distinguished on the basis of RNA levels alone.

Insights into Disease and Drug Targets

“Lastly, for genetic diseases caused by mutations in protein-coding regions, the protein information across tissues can suggest the affected organs and explain specific disease symptoms that cannot be explained by genomic studies. As such, the protein data generated in this study is expected to provide valuable insights into human biology and disease," said Dr. Michael Snyder.

Importantly, for many genes, enrichment only occurs at the protein level and not at the RNA level, so protein expression information may provide insights into the underlying disease mechanisms that cannot be identified using RNA information alone. This demonstrates the importance of collecting protein expression information for the understanding of disease phenotype. Thus, the researchers systematically investigated the protein expression patterns of genetic diseases and found many cases where disease-associated proteins are present in tissues that manifest disease-related pathophysiology; many of these would not be evident from RNA analysis.

For example, Bardet-Biedl syndrome (BBS) is a genetic disorder caused by mutations in at least 14 different genes and affects many parts of the body. BBS-affiliated vision loss, polydactyly, obesity, and other abnormalities can be explained by specific gene mutations but many are still largely unknown; tissue-specific protein expression information might explain some of the clinical symptoms. The researchers detected proteins from 11/14 BBS genes, among which seven are enriched in the pituitary and five are in the brain, muscle, heart, or liver. Abnormality of proteins in the pituitary can broadly affect developmental processes and perhaps cause obesity, diabetes, or hypogonadism observed in BBS patients. The abnormalities in proteins in the brain, muscle, heart, and liver might also contribute to defects such as intellectual disability, delayed motor skills, and conditions that involve the heart, liver, and digestive systems.

Leigh syndrome is another genetic disease that is associated with mutations in as many as 75 genes. Most of the affected proteins are involved in energy production in the mitochondria. Of the 67/75 proteins observed, 52 showed-up in metabolically active tissues, such as the heart, muscle, brain, and stomach. Some of these proteins were present in all affected tissues and some were only in one or several tissues; their different distributions might cause different tissue-related clinical symptoms. For example, the characteristic progressive loss of mental and movement abilities of Leigh syndrome is most likely related to protein abnormalities in the brain and muscle. Some individuals develop hypertrophic cardiomyopathy which could be caused by mutations in proteins present in the heart. The first signs of Leigh syndrome are vomiting, diarrhea, and difficulty swallowing -- which could be explained by the abnormality of proteins found in the stomach.

Finally, the team identified 1,329 potential drug-targeted proteins, about half of which are FDA approved drug targets. These drug-targeted proteins span 742 different tissues, and 368 are present in more than one tissue. For drug-targeted proteins present outside of the target organ, the drug may have unintended side effects in the off-target tissue. For example, valproic acid is an anticonvulsant drug that works through the inhibition of a protein in the brain. Snyder’s team showed that this drug-targeted protein is also enriched in the liver and pancreas, suggesting the underlying cause of reported liver and pancreas toxicity side effects.

“This study provides a valuable resource for us to understand human biology and diseases from proteins which are closer to phenotype. We envision some tissue specific proteins can be used as better biomarkers for diagnosis as well.” said Dr. Michael Snyder.

Find A Quantitative Proteome Map of the Human Body article here....

Prof. Michael Snyder's Lab

Prof. Michael Snyder and Lihua Jiang

Proteins – like you’ve never seen them before

Wed, 02 Sep 2020 17:52:32 GMT

The Human Protein Atlas (HPA) team plans to release a series of "Movie of the month" during 2020 and 2021. The scientific movies allow for taking a journey into the body through 3D videos that transport you deep inside various organs. The imaging is based on antibody-based profiling of tissues and light sheet microscopy.

Mentoring Party Invitation

Wed, 02 Sep 2020 17:50:50 GMT

HUPO Early Career Research initiative together with Young Proteomics Investigators Club (YPIC) invite everyone to special mentoring sessions at during HUPO Connect 2020. For the first time, the HUPO mentoring will be held online in 3 sessions on different days and times, to allow global participation.

Session 1. How to make the most out of a mentor-mentee relationship. Monday Oct 19, 14:00 UTC

Session 2. Career, family and work-life balance (during the pandemic). Tuesday Oct 20, 21:30 UTC

Session 3. Beyond academia - Reflections from industry and publishing. Wednesday Oct 21, 05:45 UTC

Speakers include B. Garcia and R. Huttenhain. See HUPO Connect 2020 program for session details.

Mentoring sessions are included in your HUPO Connect 2020 registration, so pull up a comfy chair, grab your drinks and snacks and join in the party.

Help us prepare by telling us what you need:

https://www.surveymonkey.com/r/hupoecr2020

HUPO Connect 2020 Updates

Wed, 02 Sep 2020 17:43:06 GMT

View our extensive program for HUPO Connect 2020 with 9 scientific sessions, 3 mentoring sessions, industry talks, General Assembly of Members, HPP Futures Day as well as PhD poster and ECR manuscript competition finals. Virtual posters will be available on-demand throughout the Congress. There will be different options for delegate interactions and fun activities, so don’t miss this opportunity to connect with international colleagues!

Pre-Congress Training Course
Our online Pre-Congress Training course includes 4 training topics: Proteomics 101, Proteogenomics, Post-translational modification (PTM) analysis, and Computational Tools for Functional Analysis of Proteins. The course will conclude with inspirational, short talks in a special New Technologies and New Approaches session on Friday, October 16, 2020. See detailed program here.

Early Bird Registration until Sept 28, 2020
Registration savings are still available for HUPO Connect 2020! A single registration allows access to the Pre-Congress Training course (from Sept 28) and all Main Congress activities including the Human Proteome Project Futures Day (Oct 19-22).

Upcoming Webinars

New Innovations in Proteomics
Join Chair, Anne Bendt, and Speakers, Albert Heck (Fishing Within the Proteome with Phosphate and Phosphonate Handles) and Bernd Bodenmiller (Highly Multiplexed Imaging of Tissues with Subcellular Resolution by Imaging Mass Cytometry), for our last webinar leading up to HUPO Connect 2020 on Thursday, September 24, 2020. Register today for New Innovations in Proteomics!

Note: All webinars are free for HUPO Members. Non Members can sign up for HUPO’s Mailing List during the registration process and receive complimentary registration. Learn more about these webinars by clicking here.

Call for Executive Committee Nominations - deadline extended!!!

Wed, 02 Sep 2020 17:42:08 GMT

Nominations are invited from active HUPO members with professional experience in the educational, research, or commercial activities related to the purposes of HUPO, to serve 2-year terms as treasurer or member-at-large (2 positions) on the HUPO Executive Committee, commencing January 2021. Nominations will be elected by Council vote.

For more information and to apply, view, complete and submit the HUPO Executive Committee Nomination Form with a photo of yourself, by September 15 , 2020.

2020 HUPO Council Elections - Open soon

Wed, 02 Sep 2020 17:41:22 GMT

Online voting for HUPO 2020 Council Elections will begin on Monday, September 21st and an email containing a secure election ID code along with voting instructions will be sent to all active HUPO members. If you are a HUPO member and do not receive this email check your Junk/Spam folder. Election closes on Sunday, October 18, 2019 at 23:59 Pacific Standard time (PST); be sure to submit your anonymous vote before then!

"A guided tour through neXtProt » on 22 September 2020

Fri, 31 Jul 2020 19:39:54 GMT

Working on human protein data but never had time to explore neXtProt? Want to better understand its data model or integrate its tools in your data workflow? This online course (lecture and/or practicals) is for you! Please register asap, places are limited! Visit the SIB page for more details: https://www.sib.swiss/training/course/2020-09-nextprot

HUPO 2020 Virtual Awards: Nominations are open!

Fri, 29 May 2020 17:38:35 GMT

With the development of a “Virtual HUPO 2020” congress, this year the HUPO awards will be presented online via webinar during the virtual congress .

The following HUPO awards remain open for nominations until July 31, 2020:

Distinguished Achievement in Proteomic Sciences Award ($3000, sponsored by Journal of Proteome Research – ACS Publications) recognizes a scientist for distinguished scientific achievements in the field of proteomic science.

Discovery in Proteomic Sciences Award ($3000, sponsored by Journal of Proteomics – Elsevier BV) recognizes a scientist for single discovery in the field of proteomics.

Clinical and Translational Proteomics Award ($3000, sponsored by Clinical Proteomics – BioMedCentral) recognizes a scientist for distinguished scientific achievements in the field of clinical and translational proteomics.

Nomination Deadline: July 31, 2020

Click here to review the nomination requirements and submission details.

Thank you for your nominations!

HUPO 2020 World Congress Postponed to 2021

Thu, 30 Apr 2020 15:00:50 GMT

After close monitoring of the global risk assessment by the World Health Organization of the COVID-19 pandemic, on behalf of the HUPO Executive Committee, Swedish Proteomics Society, Swedish Pharmaceutical Society and the HUPO 2020 Local Organizing Committee, we wish to share with you today that the HUPO 2020 World Congress (HUPO 2020), originally scheduled on October 18-22, 2020 in Stockholm, Sweden will be postponed to October 24-28, 2021. The location (Waterfront Congress Centre in Stockholm, Sweden) will remain the same.

The postponement was based on multiple factors, including but not limited to, the current travel restrictions put in place and, importantly, the toll currently being placed on our health care community. These restrictions significantly affect the ability of delegates, speakers, presenters, sponsors and exhibitors to participate fully in HUPO 2020. This decision also underlines our commitment to containing the virus and preventing further sickness and loss of life, as per WHO recommendations.

Although the postponement comes as a great disappointment, we are ready to embrace the challenge! We want to ensure you stay connected with what's happening in proteomics, which is why our team is excited to announce the first-ever international HUPO virtual experience! We will be providing a series of virtual meetings in fall of 2020 which amongst the sessions planned will include one to highlight the role of proteomics in tackling many key aspects of the COVID-19 pandemic.

Due to the rapidly evolving nature of the pandemic, we invite all delegates and industry partners to read our FAQs and monitor your emails, as well as the congress website, for specific information on the new Congress timeline.

The Local Organizing Committee with the support of the Swedish Proteomics Society, Swedish Pharmaceutical Society and HUPO are committed to bringing you a HUPO World Congress as never before and look forward to seeing you in 2021!

In the meantime, please stay safe and healthy.

Stephen Pennington
HUPO President

2020 HUPO Council Election - Nominations close in 2 weeks!

Fri, 17 Apr 2020 20:54:58 GMT

Don't miss the chance to submit your candidacy to become a HUPO Council member for a three-year term (2021-2023). Complete the 2020 Elections Nomination Form (available here) and submit it to office@hupo.org before 30 April 2020.

The current council list can be found here:2020 HUPO Council Election

The deadline to receive nominations is 30 April 2020.

A Call for (Pathway) Reviewers

Fri, 31 Jan 2020 00:56:55 GMT

Henning Hermjakob, European Bioinformatics Institute, UK

Biomolecular pathways are a key tool to put proteomics results into context, and pathway databases are often the first port of call to make sense of long lists of identifications and quantitations. Reactome (https://reactome.org) [1] is an open source, open data knowledge base of curated human pathways. While Reactome employs full time curators, we depend critically on voluntary domain experts who provide their time and knowledge to ensure quality and coverage of the pathways annotated in the database. Similar to manuscript reviewers, these essential community contributors are hard to attract, and the Reactome team would like to reach out to the HUPO community to contribute to the extension and validation of Reactome content. Recently, we have added features that allow to search for contributors by name, and for them to claim their contributions to their ORCID (https://orcid.org/) profile with a few clicks [2], contributing to efforts to provide credit for open data.

So, if you have a favorite pathway, please check if it’s already perfect in Reactome, and if not, click on https://reactome.org/community/collaboration to provide your expertise, and to support your future pathway analysis!

When you give presentations please disseminate this important message- using the slides included here.

Example of a Reactome pathway overview diagram (free to download as vector graphic).

1: Jassal B, et al. The reactome pathway knowledgebase. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. PubMed PMID: 31691815.

2: Viteri G, et al. Reactome and ORCID-fine-grained credit attribution for community curation. Database (Oxford). 2019 Jan 1;2019. pii: baz123. Doi: 10.1093/database/baz123. PubMed PMID: 31802127.

Proteomics: Sample Preparation, Mass Spectrometry and Data Analysis Course - Indian Institute of Technology (IIT) Bombay

Sat, 02 Mar 2019 00:21:04 GMT

Sanjeeva Srivastava, IIT Bombay, India

On February 5 – 7, 2019 the Continuing Education Programmes (CEP) at IIT Bombay hosted a Proteomics course titled “Proteomics: Sample Preparation, Mass Spectrometry and Data Analysis”. Participants prepared their own samples for protein identification, label-free quantification and iTRAQ-based quantitative proteomics analysis. While the participants learnt new techniques, the proteomics team from IIT did meta data analysis, results for coverage and reproducibility in assays. Click here to view the event photos.

Human Personal Omics Profiling (hPOP) - Assay Invite

Wed, 12 Dec 2018 23:16:06 GMT

A Message from hPOP - Assay Invite

The hPOP project to profile people from around the world has been highly successful in the sample collection. We have collected samples from each of the three regions: Boston (Pilot n = 31 individuals), Taipei (N = 106), Dublin (n = 115), Orlando (n = 84). Plus to increase North American numbers we have collected samples from the Bay area (n = 40).

We are now ready for the analyses. On a google spread sheet we list possible assays. We are looking for volunteers to help carry them out. Feel free to suggest additional assays. Our goal is to get these assays done in the next 2-3 months and then analyze the data and present the results at the next HUPO meeting in Australia. The analyses will take some time because there is lots to do we need to do age correction, BMI, etc. We suggest discussing results/analyses on consortium calls starting in January. Note the Snyder lab signed up for many assays but if there are volunteers to take over some of them that would be fine (we want to make sure that a basic set of analyses is done).

We are also building an interactive database to get the data back to participants.

1. Please sign up for assays on the google spread sheet here.

2. Send any and all comments to us at sahadi@stanford.edu.

Let us know if you would like to participate in any of the consortium calls. This is a very unique project and open access resource-we hope to get a high profile paper out of this.

Norman G. Anderson (1919-2018)

Tue, 11 Dec 2018 17:53:06 GMT

Norman Anderson passed away November 22, 2018 after a short illness, five months before his 100th birthday. He is known both for visionary Big Science projects (the Molecular Anatomy Program, the Human Protein Index, and Rapid Response to Viral Pandemics) and for a series of widely-used bioanalytical inventions (the zonal ultracentrifuge, the centrifugal fast analyzer, large scale 2-D electrophoresis, and virus purification, which was his creative focus late in life). His career spanned military service in World War II (US Navy), advanced degrees (Duke University), National Laboratories (Oak Ridge and Argonne), commercial biotechnology (Large Scale Biology Corp), and non-profit foundations (Viral Defense Foundation), producing more than 250 publications and 35 patents.

Norman Anderson was raised in a religious family of St. Paul MN, in which his father, brother and both sisters pursued careers in the Norwegian Lutheran church. Joining the Navy during World War II, work in underwater photography, eye movement tracking during instrument flight, and on submarines and blimps, expanded his horizons and allowed him to develop novel equipment and ideas. During the war, he met and rapidly married Mary Lloyd Glidewell, daughter of a prominent lawyer in Reidsville, NC, who provided the genial southern atmosphere that sustained him for their 77 years together. Mary Lloyd encouraged him to follow his scientific interests as a graduate student at Duke, instead of accompanying his Navy friends to Hollywood as a photographer, and after a PhD in cell physiology, Norman accepted a fellowship at Oak Ridge National Laboratory where he remained for 20 years. At Oak Ridge, he developed a plan for the complete fractionation of human cells, and to this end developed the zonal ultracentrifuge (including systems for large scale influenza virus purification still used to produce safe vaccines today), the centrifugal fast analyzer (subsequently commercialized by multiple companies for clinical laboratory testing), and high-pressure liquid chromatography systems.

After a brief interlude at the Medical University of South Carolina, Dr. Anderson moved to Argonne National Laboratory near Chicago, where, together with his son Leigh Anderson, he pioneered the use of large-scale 2-D electrophoresis to catalog the human proteins. The potential of this technology led them to start Large Scale Biology Corp. (LSBC), leading to the complete automation of 2-D electrophoresis and the creation of protein databases, as well as development of a large-scale centrifugal oligonucleotide synthesizer (PCOS). After merging with a California-based protein expression company, LSBC completed a highly successfully IPO in 2000.

Over the past 15 years Dr. Anderson focused his attention on the problem of detecting newly emerging viruses and rapidly creating vaccines to prevent their spread as epidemics. His vision of a Manhattan Project-style approach to this existential challenge to civilization highlighted the differences between modern mechanisms of grant-based scientific research and the scale, commitment and speed possible in the context of a World War.

Dr. Anderson received a number of awards including the Distinguished Clinical Chemist Award from the International Federation for Clinical Chemistry (1990); the 1983 Pittsburgh Analytical Chemistry Award (1983) for work in high resolution two-dimensional electrophoresis (shared with N. Leigh Anderson); an Docteur Honoris Causa, University of Nancy, France; the John Scott Medal and Award for the invention of the zonal ultracentrifuge (1972); the Atomic Energy Commission Citation and Gold Medal for the invention and development of the K-II vaccine-purification ultracentrifuge (1972); the Preis für Biochemische Analytik, awarded by the Deutsche Gesellschaft für Klinische Chemie for the invention of the centrifugal fast analyzer (1972); and a U.S. Navy Special Citation for outstanding work as a combat photographic officer in the submarine service in the Pacific during WWII (1946).

Norman Anderson is survived by his son (Leigh Anderson), with whom he collaborated in proteomics research for more than 40 years, Leigh’s wife Constance Seniff, and his daughter (Beth Anderson, successively a ballerina, rock musician, scientific instrument builder and science animator), and her husband Douglas Huff. Mary Lloyd died six months before him, which was a great blow. Norman is fondly remembered by a host of co-workers, students and neighbors in whom his perpetual enthusiasm excited a profound interest in science.

Press Release: Incoming Chair of the Human Proteome Project

Tue, 06 Nov 2018 01:16:14 GMT

Following an international search, the Human Proteome Organization (HUPO; www.hupo.org) has recently selected cancer researcher Mark Baker from Macquarie University, Australia as the incoming Chair of the Human Proteome Project. Effective January 2019, Mark will succeed pioneering physician-scientist Gilbert (Gil) Omenn from the University of Michigan, USA who led this emerging global collaborative project since launch in 2010.

The Human Proteome Project brings together an impressive array of research teams from around the globe, focused on achieving highly-confident detection and identification of all the expressed proteins that are predicted to be coded by the human genome. The Human Proteome Project then aims to characterize the proteome’s sequence, splice and chemical modifications that alter locations, function and interaction. The Human Proteome Project is cooperating with the broader scientific community to annotate biological, chemical, cellular and disease aspects of the human proteome using rapidly-evolving technologies.

One outcome will be a comprehensive “map” of protein pathways and networks that will demonstrate the indispensable role our proteomes play in precision medicine - because we know it is impossible to predict these dynamic, structural and functional details of biology just by sequencing our genomes.

Sustained progress through the Human Proteome Project will noticeably enhance our understanding of human biology at the molecular level, lay solid foundations for monitoring health and the development of new preventive, diagnostic, prognostic and therapeutic interventions in disease, and increase our biological understanding of what it means to be human.

Contacts for Comment:

Professor Mike Snyder - HUPO President, Stanford University, USA mpsnyder@stanford.edu

Ms Chelsea Prangnell - Manager, Human Proteome Organization chelsea@hupo.org

2018 HUPO Council Elections - Candidates Announced

Fri, 29 Jun 2018 16:08:17 GMT

The Nominations and Elections Committee of the Human Proteome Organization presents the official slate of candidates for the 2018 HUPO Council election. HUPO would like to thank all candidates standing for Council election for a three-year term beginning in January 2019 (2019-2021). The election period for HUPO Council is September 5 - September 30, 2018.

In September, all active HUPO members will receive an email containing online voting instructions with a secure election ID code. Electors will simply click on the link provided to cast their anonymous votes.

The slate of candidates is now available here. We encourage you to review the slate of candidates prior to the election opening date on September 5, 2018.

Thank you,

Henning Hermjakob

Chair, HUPO Nominations and Elections Committee

Institut Pasteur – INCEPTION Annual Call for New Junior Group Leaders

Wed, 06 Dec 2017 22:16:45 GMT

Deadline January 14, 2018: Institut Pasteur has launched an international call for junior candidates wishing to establish new independent research groups in the cutting edge interdisciplinary environment of its campus in Paris, France. This year the call will be focused on the topics associated with the INstitut Convergence entitled “Emergence of Pathologies Through Individuals and populatiONs” (INCEPTION program). Read on here.

Interview with Professor Albert Heck

Mon, 23 Oct 2017 17:54:51 GMT

HUPOST: Can you tell us what this prize, which is referred to as the Dutch Nobel Prize, means for you, and for the field?

Heck: The Spinoza prize is the most prestigious Dutch science award, and is given annually to three to four researches, selected from all disciplines of science.

It is of course an enormous honour to be awarded this prize, and while it’s known as the Dutch Nobel Prize, it evidently does not compare to the real Nobel. Nevertheless, it comes with a 2.5 million euro budget, to be spend freely for research, so it is a very strong driver for creativity and innovation.

Although a personal prize, I think this award is also an award for my group and the field, because the prize is an implicit recognition for the importance and impact of analytical chemistry, biomolecular mass spectrometry and proteomics.

HUPOST: You have your own Wikipedia page, and a list of prestigious awards to your name. What would be your advice to young researchers who want to make a difference?

Heck: If you want to make a difference, evidently you should keep up with the literature, so you know what lives in the field, but that knowledge should not stop you from doing the unexpected and you should always look for unexpected findings. In my view, these are the key to innovation and succes. And I try to encourage everyone not to be a follower; try doing something different than the other labs in your field. When you have a keen eye for the unexpected, and do original work, then you will be able to contribute unique findings and can make a difference. And find the right environment, as good mentors are way more important than a good lab-infrastructure.

HUPOST: When a researcher pursues something different, the research can also fail. Do you have any tips on how to deal with such setbacks?

Heck: We should not fear failure. In fact, most scientific experiments end in failure. There’s no satisfaction to be had from planning an experiment for which the outcome is already known. And never forget: after you encounter a few failures, the next success will taste so much sweeter!

HUPOST: If you were a starting scientist today, what topic would you choose?

Heck: My main driver is very broad: understanding how life works at the molecular level. Of course, ‘life’ is very diverse, and there’s much to study. But right now, I would love to look more into how the brain works at the molecular level. This is an area we still understand so little about.

In general, I strongly believe that everybody needs to find something that strongly attracts their interest, as it is very important in science to work on a topic you really care about.

HUPOST: Your lab has also produced very nice short movies to introduce science to the general public; how important is this outreach?

Heck: I think it is very important and exciting to outreach to the general public. But I have also learned that you need to have a strategy for these movies, so that they hit their mark. Importantly, it is also very much fun to make such movies. Overall, I believe that if you study proteins, and are excited about proteins, as I am, that you should also spread this excitement! And because the general public will not read our papers in Nature and Science, such movies are a great way to bring our research to a broader audience. It is particularly rewarding to see that some of our movies are featured in the Washington Post, but these are used in classrooms as well. If you make a movie, try to make them as multi-purpose as possible.

Movie links:

http://www.hecklab.com/molecularclock/

https://www.youtube.com/watch?v=1G6jTGAfgUc&feature=youtu.be

HUPOST: While on the subject of classrooms, do you believe that knowledge about proteomics should move into classrooms?

Heck: Yes, of course, although I would prefer a more overall view: we should be teaching more insight into life at the molecular level in the classrooms, and this should be based on knowledge of the entire cast of macromolecules (DNA, RNA, proteins) that feature in this grand spectacle we call live.

I also think that the progress of scientific knowledge in the life sciences are taking too long to reach the classrooms, and that is a pity. All the more so because the knowledge is so interesting and inspiring. A great example is the gene transcription machinery, which is not only a fundamental process in all life, but it also combines proteins, DNA, and RNA in a fascinating molecular machine.

HUPOST: Which of your contributions to the field gave you the most satisfaction?

Heck: That’s a difficult question. It’s like being asked to pick the favourite child amongst your children. But I really enjoy technology development. This because there is great satisfaction in receiving mails from other researchers that write to let you know that your technology has helped them do their research. Science is all about sharing after all, and when people pick up technologies that you’ve developed, and it works for them, that is extremely motivating.

In addition, new technologies often lead to breakthrough findings in biology. For instance, the EThcD technology we developed has led to the discovery of widespread proteasomally spliced HLA peptides, which shook up the field of immunology. So I really like the ability of technological breakthroughs to lead to a new understanding of biology, which is, after all, the goal!

Paper reference: http://science.sciencemag.org/content/354/6310/354

MS-Pillar Phosphopeptide Challenge

Sun, 17 Sep 2017 20:21:35 GMT

The MS-Pillar of the Human Proteome Project invites all HUPO members to participate in the Phosphopeptide challenge. The MS Resource Pillar has partnered with SynPeptide Co. Ltd in Shanghai (www.synpeptide.com) to develop a complex set of human phosphopeptides (Ser, Thr or Tyr) singly and multiply phosphorylated) and their unphosphorylated counterparts that can be used for method development and verification for phosphopeptide enrichment, sequence analysis by mass spectrometry and bioinformatic evaluation. The first stage of this initiative is for interested members of the HUPO community to obtain a set of the peptides and apply their own methods and bioinformatic analysis to fully characterize the peptides as a neat mixture and in a tryptic digest background. As a result of this collaborative endeavor, multiple purification schemes, analytical protocols and data processing strategies will be evaluated, making it possible to determine the approach(es) that provide the highest coverage of phosphopeptides in the mixture.

By partnering with SynPeptide the peptide sets are being provided free-of-charge to all HUPO members, with the understanding that the analytical and data processing methods and results will be returned to the MS Resource Pillar committee so they can be collated and reported at the HUPO 2018 meeting. Free aliquots of the peptide mixtures can be obtained at the HUPO2017 Congress in Dublin from Peter Hoo from the SynPeptide stand. MS-Pillar Chair Prof. Sue Weintraub will make a short presentation on Monday September 18 at 16:30.

Press Release: HUPO 2017 Global Leadership Gala Dinner

Wed, 06 Sep 2017 19:10:39 GMT

The Human Proteome Organization (HUPO) and Prof Steve Pennington, UCD, chair of the organizing committee of HUPO2017 (the 16th HUPO World Congress) in collaboration with the National Cancer Institute’s (NCI) International Cancer Proteogenome Consortium (ICPC) announce that they will host a HUPO2017 Global Leadership Gala Dinner on Saturday 16th September. The event is catalyzed in part, by the Cancer Moonshot initiative. The organizers are delighted that the 47th Vice President of the United States of America Joseph R. Biden Jr. will deliver a keynote address at the dinner on the theme of “International Cooperation in the Fight Against Cancer.”

The evening dinner event being held in the Royal College of Physicians in Dublin will bring together the world’s leading proteomic and proteogenomic researchers including those working on cancer research in the company of government, academia and industry leaders. The event will focus on both raising awareness of HUPO and its activities, and advances in proteomics and their impact on human health, as well as the ICPC which currently comprises 11 countries and seeks to encourage more institutions to join this global partnership.

“Every day, every minute matters to patients and we must bring that sense of urgency to our cancer research and care systems.”

Joe Biden

Catalyzed by the efforts of the Cancer Moonshot launched in 2016 by the 47th U.S. Vice President Joseph R. Biden Jr., this year’s HUPO Annual World Congress (HUPO2017) will encourage further collaborations among countries and institutions that represent the great diversity of people and of cancers. Echoing the call of the Cancer Moonshot to accelerate progress against cancer around the world, ICPC (International Cancer Proteogenome Consortium) has currently signed Memorandums of Understanding with 11 countries, encompassing multiple institutions that have pledged to publicly share their proteogenomic data (hosted by the U.S. National Cancer Institute) to accelerate the understanding of common and rare cancers around the world. ICPC teams use an integrated proteogenomic approach, as previously shown by the U.S. National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) to provide more information and insight into cancer’s development and growth, with the aim of leading to better patient care.

For further information and details, contact:

HUPO2017: Professor Steve Pennington: stephen.pennington@ucd.ie

HUPO: Chelsea Prangnell: chelsea@hupo.org

U.S. National Cancer Institute: ncipressofficers@mail.nih.gov

Call for HUPO Success Stories

Tue, 20 Jun 2017 18:00:00 GMT

Dear HUPO colleagues,

HUPO takes knowledge transfer seriously in the current increasingly competitive communication and funding circumstances. The HUPO Marketing Committee is assembling a series of exciting scientific/clinical/technological Success Stories that either proteomics and/or HUPO have delivered.

The taskforce (Mark Baker (chair), Christoph Borchers, Michelle Hill, Pierre Legrain, Charles Pineau and Lennart Martens) asks you to illustrate/describe the Success Story. In addition, the committee will seek comments about impact from eminent researchers and industry alike. These Success Stories will be assembled annually into a constantly growing portfolio, and when each story is complete it will be made available in high-quality print as pdfs, through Facebook, LinkedIn, Twitter, on our integrated HUPO/HPP website and through our HUPO and HPP newsletters.

The committee will accept Success Story suggestions at any time, preferably through the following web-based nomination form:

http://tiny.cc/HUPO_SuccessStories

Scientists, clinicians and industry are all encouraged to submit.

Please feel free to communicate any proteomics/HUPO breakthrough Success Story.

Thanks.

Best always,
Mark

Mark S. Baker

Past President | Human Proteome Organization

New Open Access Publication describing the neXtProt peptide uniqueness checker

Mon, 29 May 2017 21:29:50 GMT

The neXtProt peptide uniqueness checker maps uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. The use of this tool is recommended in the latest HPP guidelines as it can be used to define which peptides can be used to validate the existence of human proteins. The tool is described in the recently published Bioinformatics Application Note https://doi.org/10.1093/bioinformatics/btx318.

C-HPP NEWSLETTER No. 6

Wed, 17 May 2017 17:01:00 GMT

The 6th newsletter of the Chromosome-centric Human Proteome Project is now available online, read it here.

In this issue:

Editorial
C-HPP Leadership Update
C-HPP Principal PIC
A Brief Introduction Of New PIs and Plans
JPR SI Call For Papers
Working Group Formation of C-HPP
Briefings in the 2016 C-HPP Workshops
Future C-HPP Workshops

Join the hPOP (Human Personalized Omics Profiling) project at HUPO 2017

Wed, 10 May 2017 20:47:42 GMT

The hPOP (Human Personalized Omics Profiling) project is designed to study the variance of molecular markers across a large number of participants. Recent advances in high throughput technologies allow profiling of thousands of analytes within a single experiment. These measurements could potentially be used to diagnose disease early, monitor treatment progression and stratify patient groups to ensure each individual obtains the treatment best suited to their needs. This personalized approach to medicine would include continuous monitoring of thousands of parameters over a whole lifetime. However, in order to be able to interpret such data, we need to have a better understanding of the underlying natural variation of these molecular parameters in health and disease. Only if we know the natural ranges of individual analytes, the expected responses to perturbations and the long-term trends in their levels, can we draw meaningful conclusions from comprehensive personalized profiling.

In this project, we aim to use a multi-omics approach to study the genome, epigenome, transcriptome, proteome and metabolome of a large number of healthy volunteers. The hPOP project will be launched officially at the 2016 HUPO in Taipei where samples from several hundred people will be collected. The current protocol includes sampling of blood, urine and stool after overnight fasting. Additionally, a detailed questionnaire about food habits, personal health, physical activity and stress levels will be filled out by each participant. All data will be made available to the scientific community under public domain which will allow multiple research groups to use the generated data in their own studies and perform their own analysis of the data.

To find out more or to join the hPOP mailing list, visit the website.

NCI-CPTAC DREAM PROTEOGENOMICS CHALLENGE

Wed, 10 May 2017 19:25:22 GMT

Proteogenomics, integration of proteomics, genomics, and transcriptomics, is an emerging approach that promises to advance basic, translational and clinical research. By combining genomic and proteomic information, leading scientists are gaining new insights due to a more complete and unified understanding of complex biological processes.

Advanced bioinformatics approaches are needed to entirely use the complete information spectra acquired in genomics, transcriptomics and proteomics studies. A DREAM Challenge offers a chance to crowdsource the analysis of numerous rich data sets at once (one of the largest public repositories of proteogenomic sequence data) and thereby compare aspects of various methods to better understand biological features that drive early cancer progression.

To this regard, the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) program, in partnership with DREAM Challenges, announce the NCI-CPTAC DREAM Proteogenomics Challenge (estimated launch date is mid-June). The aim of the challenge is to encourage the generation of computational methods for extracting information from the cancer proteome and for linking those data to genomic and transcriptomic information. The goal is to predict proteomic and phosphoproteomic data from multiple other data types. Method performance will be blindly evaluated using a previously unseen validation dataset generated by CPTAC.

DREAM Challenge will be run in the Google Cloud, and provide a prize award sponsored by the NVIDIA Foundation. Nature Methods also supports the submission of an overview paper of the Challenge, contingent on a standard evaluation process.

For Registration, click here

Please visit the DREAM website for further details on DREAM challenges, including history, previous challenges and FAQs.

Call for applications - HPP Clinical Scientist Travel Grants

Wed, 26 Apr 2017 17:33:06 GMT

Dear HUPO colleagues,

The HPP is reaching out to clinical scientists or clinicians who are using or consider using proteomics for their research projects. HPP is supporting six (6) clinical scientists with a travel grant to attend the 2017 HUPO World Congress in Dublin, Ireland that will take place from September 17-21, 2017.

Travel grant recipients will receive USD $1,000 to offset travel and hotel costs in addition to complimentary congress registration. The recipients are expected to actively participate in the HUPO congress, particularly in the activities and discussions related to the HPP. Further information on the HUPO 2017 congress and HPP activities in Dublin can be found at http://hupo2017.ie/.

Application deadline: Friday, June 30, 2017

For more information and application instructions visit https://hupo.org/HPP-Clinical-Scientist-Travel-Grants.

HUPO2016 Taipei: Reports from young scientists

Wed, 19 Apr 2017 15:30:00 GMT

Congratulations to the HUPO2016 Taipei PhD abstract competition winners!

Christopher Ashwood (Macquarie University, Australia)

At HUPO, I saw innovative techniques that I had not been exposed to before this conference. I felt inspired by watching a great range of presentations by world-renowned experts in their area of expertise and particularly enjoyed the sessions on glycoproteomics. During breaks between sessions, I was exposed to a huge range of posters from researchers all around the world.

Thanks to the mentoring pre-conference workshop, I learned about the current challenges and expectations in academia. My PhD experience has also been improved by learning about the best current practices in the field of proteomics. Due to this conference, I’ve been able to be up to date on the most recent advances in instrumentation as well as using existing technology to address well-known challenges. The most important point I took away from this conference was the importance of bioinformatics in processing big data sets for more effective biological studies.

During my attendance of HUPO 2016, I felt encouraged that my research area is important to HUPO and thankful for the organising committee for setting up this conference.

Margherita Dell´Aica (ISAS, Germany)

Last year I had the unique experience to attend the HUPO World Congress in Taipei. The program was packed with exciting talks covering cutting edge research, e.g. Technological Advancements, PTMs, Computational Omics and Cancer Research, rendering it the ideal opportunity to promote my own work. The key-note lectures provided deeper (historical) insights and I enjoyed listening to top speakers I only knew from articles.

I am very pleased that I became one of three winners of the HUPO PhD abstract competition. Getting more actively involved into this super-international community and the great experience to promote and defend my work in front of leaders in the fields truly were inspiring and motivating.

The Conference atmosphere was remarkable, such as the kindness of the Taiwanese, the food, the beauty of Taipei’s cosmopolitan streets and the relaxing view of Sun Moon Lake.

Altogether, participating the HUPO 2016 provided me high professional feedback, novel ideas to improve my work, to collaborate with other scientists, and to further pursuit my scientific goals and career. I will definitely participate again in coming years.

Zhiduan Su (University of Sydney, Australia)

It is my great honour to attend 15th HUPO congress in Taipei, which is also an unforgettable experience to me. I also need to thank HUPO 2016 Committee to give me an opportunity to present my study in this congress. My project is about redox proteomics and cysteine oxidations and so far focused on metabolism-disordered cell models. It was really a fantastic and precious occasion that almost all "redox proteomics stuff" could get together and exchange opinions with each other during the congress that might contribute to better understanding of our studies. Also, I was able to meet a few "big guys" and listened to what they were doing recently and what they wanted to do next, which were relevant to the present and future of proteomics progress. Certainly, meetings with old friends during the conference were the memorable moments in my life as well.

HUPOST April 2017

Mon, 10 Apr 2017 20:23:15 GMT

HUPO 2017 Abstract Extension

Abstract submissions to the 16th Human Proteome Organization World Congress have been extended to 3 May 2017. Read more >

ECR Manuscript Competition

The Early Career Researcher (ECR) Initiative of the Human Proteome Organization is pleased to announce the 3rd ECR Manuscript Competition to take place at HUPO 2017 in Dublin! Deadline 5 June 2017. Read more >

PhD Abstract Competition

Once again, HUPO is holding a PhD Abstract Competition. 8 abstracts will be selected based on excellence to have a short oral presentation at HUPO 2017 in Dublin. Deadline 3 May 2017. Read more >

HUPO Elections

HUPO is seeking candidates to serve on the HUPO Council for three-year terms beginning January 2018 (2018-2020). We invite you to nominate yourself and other scientists from your region. Deadline 30 April 2017. Read more >

Editor's Note

Welcome to the new HUPOST! As Emma Lundberg, our much-appreciated outgoing Editor, announced in the previous HUPOST, we updated the format for 2017. Key points are now included in the email, and our circulation has broadened to reach an even wider audience. HUPOST’s frequency has also increased to every two months, alternating between a short and snappy overview of current news, and an extended version that covers interesting developments in the field of proteomics.

Speaking of interesting developments, allow me to remind you that the HUPO 2017 World Congress in Dublin on 17-21 September is now only 5 months away! Abstract submissions will now be accepted until 3 May, so you can still join us and share your latest work. I very much look forward to hearing about it, and to meeting you, on the Emerald Isle in September!

Meanwhile, enjoy the new HUPOST, and make sure to let us know at office@hupo.org when you have something to share! As always, you can find us on social media: Facebook, Twitter, and LinkedIn.

Cheers, Lennart Martens - HUPOST Editor

President's Message

There has never been a more exciting time for proteomics. We can rapidly measure thousands of molecules and posttranslational modifications, and there are large initiatives such as the Cancer Moonshot and Gene-Tissue Expression Project in which proteomics will make an important contribution. As technological advances continue proteomics will play an increasing role in large-scale influential projects.

A valuable part of all of these efforts is the Human Proteome Project (HPP; 1) which aims to map the proteome parts lists: protein coding genes, splice and allelic isoforms. It also aims to advance the proteomics of a wide range of human biology and disease, for example, cardiovascular disease, diabetes, cancer. With respect to the latter, we are assembling a list of popular proteins for each major human disease (2).

The HUPOST is HUPO’s forum for disseminating advances in our field. We hope to keep the community abreast of the latest advances and technologies.

Cheers, Mike Snyder - HUPO President

1) Advances of the HUPO Human Proteome Project with broad applications for life sciences research. Omenn GS. Expert Rev Proteomics. 2017 Feb;14(2):109-111. doi: 10.1080/14789450.2017.1270763. Epub 2016 Dec 22. No abstract available. PMID: 27935328

2) Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. Lam MP, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DC, Su AI, Ge J, Van Eyk JE, Ping P. J Proteome Res. 2016 Nov 4;15(11):4126-4134. Epub 2016 Jul 19. PMID: 27356587

Call for Council Candidates | HUPO Elections 2017

Thu, 30 Mar 2017 15:00:00 GMT

Dear HUPO Members,

I am seeking candidates to serve on the HUPO Council for a three-year term that will begin January 2018 (2018-2020).

Each Councilor must be a current HUPO member who is a scientist from the public or private sector with at least ten (10) years of professional experience in educational, research or commercial activities related to the purposes of HUPO. We invite you to nominate yourself or other scientists from your region - Central region (Europe/Africa), Eastern region (Asia/Oceania), and Western region (Pan-America). Please check with your nominee to be sure they are willing to stand for election.

To nominate a colleague or yourself please complete the 2017 Elections Nomination Form (available here) and submit it to office@hupo.org before 30 April 2017.

If you nominate a colleague please note they will be asked to confirm their willingness to stand for election. The current council list can be found here.

Thank you for your support,

Henning Hermjakob

Chair, HUPO Nominations and Election Committee

2017 HUPO Council Nomination Form
Deadline to receive nominations: 30 April 2017

Cardiovascular Initiative Workshop: Moving to Precision medicine: solving cardiovascular disease

Tue, 21 Mar 2017 15:00:00 GMT

Dear HUPO Members,

The Human Proteome Organization is pleased to the announce the HUPO-endorsed Cardiovascular Initiative Workshop. The workshop features outstanding scientists from across the HUPO/HPP community. View the programme online.

The workshop takes place on 2 April 2017, during the Proteomic Forum in Potsdam, Germany. For more information, and to register, visit http://www.proteomic-forum.de/ or contact dgpf@conventus.de.

Best wishes,

Christoph Borchers

Chair, HUPO Marketing Committee

Call for nominations - HUPO 2017 Award Nominations Now Open!

Tue, 14 Mar 2017 15:00:00 GMT

The Human Proteome Organization presents awards annually at the World Congress. The HUPO 2017 World Congress is in Dublin from September 17-21. Award recipients will present a brief talk during the Congress award ceremony. These distinguished awards recognize the outstanding efforts of individuals (or groups) advancing the field of proteomics. Nominations are done through an online submission form and no supporting documents or attachments are required.

You are invited to nominate award candidates!

Nomination Deadline: April 17, 2017

Nomination Requirements

HUPO is now accepting nominations for the following awards:

Distinguished Achievement in Proteomic Sciences Award ($3000, sponsored by Journal of Proteome Research - ACS Publications) recognizes a scientist for distinguished scientific achievements in the field of proteomic science.

Discovery in Proteomic Sciences Award ($3000, sponsored by Journal of Proteomics - Elsevier BV) recognizes a scientist for a single discovery in the field of proteomics.

Science and Technology Award ($3000, sponsored by the HUPO Industrial Advisory Board) recognizes an individual, or team (of up to three people) in private industry who played a key role in commercialization of a proteomics technology, product or procedure. The emphasis for the award is on making the technology, product or procedure widely available, which is different from the basic scientific invention.

Clinical and Translational Proteomics Award ($3000, sponsored by Clinical Proteomics - BioMedCentral) recognizes a scientist for distinguished scientific achievements in the field of clinical and translational proteomics.

Distinguished Service Award ($3000, sponsored by HUPO) recognizes an exemplary member of the proteomic research community whose dedicated service has made indispensable contributions to the organization and mission of HUPO.

Success Story - Cancer Moonshot at HUPO

Mon, 06 Feb 2017 16:00:00 GMT

A real success story of international collaboration through HUPO was the launch of the International Cancer Proteogenome Consortium (ICPC) during the 2016 HUPO Congress in Taipei.

Story by Michelle Hill, B/D-HPP Newsletter Editor

Some of the ICPC representatives at HUPO 2016 in Taipei. From left: Daehee Hwang (South Korea), Ruedi Aebersold (Switzerland), Christoph Borchers (Canada), Henry Rodriguez (USA), Albert Sickmann (Germany), Mark Baker (Australia), Chia-Jung Yu, Yu-Ju Chen, Min Daw Tsai, Chen-Yang Shen (Taiwan).

This exciting development was grounded on ongoing collaboration between the Cancer Initiative of the B/D-HPP and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of The United States National Cancer Institute (NCI), and nurtured through years of work at HUPO Congresses. Following the first announcement in Australia in July 2016, an additional 7 countries now joins the initiative to form the International Cancer Proteogenome Consortium (ICPC). This is a real success story of international collaboration catalyzed by HUPO. Two of the leaders tell of the story.

Read the full story in the B/D-HPP Newsletter | Issue 1, 2017

Completing the ~20,000 proteins that make us human: new database accelerates our understanding of the role of more human proteins in health and disease

Tue, 24 Jan 2017 16:00:00 GMT

Media Release from Macquarie University - 23 January 2017

The newly released MissingProteinPedia database collates information about proteins in unprecedented ways, allowing Human Proteome Project scientists to gain a deeper understanding of how our proteins work together to make every human an individual.
While about 20,000 genes code for proteins in the human body, the new database is aiding in the identification of 2,949 “missing” human proteins that are still waiting in the wings and are yet to be proven to exist by high fidelity measurements.
The database, made by scientists at Macquarie, will be a powerful tool in helping all researchers pinpoint every protein found in the human body and how these interact, with potential repercussions for better understanding many diseases.

Much remains to be understood about how proteins in the human body works in unison; however a newly developed resource is giving scientists a more complete picture of how the proteome makes us uniquely human. MissingProteinPedia, a database developed by a collaborative research group lead by scientists at Macquarie University, could not only help researchers learn more about the location and use – termed ‘expression’ – of specific proteins in the body but also how they interact to make us human. It will also help to pin down those proteins which are still ‘in the shadows’, with implications for several diseases.

Dr Shoba Ranganathan and Dr Mark S Baker

Photographer credit: Paul Wright

“While we know a lot about individual proteins, the larger picture of how these proteins work together to make an individual person is a difficult concept to explore. Although we are developing new technologies to test when, where, why and how proteins are expressed, we still need some way of tying all the biological information together so that we get a clearer picture of how proteins work together to turn us into an individual human being,” explained Professor Mark Baker, lead author of the missing protein study.

“Our team developed MissingProteinPedia to gather all the scattered and incomplete information about what the Human Proteome Project calls missing proteins. This includes the 2,949 proteins that, despite rigorous testing, are still ‘in the shadows’ and haven’t yet been proven to exist,” he added.

The tool accelerates the discovery of many missing proteins, particularly those in elusive protein families, with potentially vast consequences for human disease.

“In order to understand how a disease progresses we need a detailed picture of how all proteins work in a healthy individual, so that we can understand what triggers the development of diseases,” explained senior author Professor Shoba Ranganathan.

“MissingProteinPedia has uncovered substantial evidence for many hard-to-detect proteins for which small amounts of information have taken years to gather. The very fact that we have come so far in such a short time bodes well for our understanding of complex human diseases such as cancer,” she added.

The researchers will make the database a community-driven, citizen-science project where everyone can help in the discovery of human missing proteins and their role in health and disease.

Baker, Mark S; Ahn, Seong Beom; Mohamedali, Abidali; Islam, Mohammad T; Cantor, David; Verhaert, Peter D; Fanayan Susan; Sharma, Samridhi; Nice, Edouard C; Connor, Mark and Ranganathan, Shoba. Accelerating the Search for the Missing Proteins in the Human Proteome.

Media Contact: Dr Megan Wright | T: +61 (2) 9850 1055 | E: megan.wright(at)mq.edu.au | A copy of this release will be available online at www.mq.edu.au/newsroom

Bioinformatics Hub at the HUPO 2016 World Congress

Thu, 17 Nov 2016 21:53:37 GMT

The Bioinformatics Hub is a place where bioinformaticians gather together with three aims: (i) to provide their advice, knowledge, and support to anyone with a relevant question; (ii) to discuss current issues and challenges in proteomics informatics with the entire community; and (iii) to work on interesting, synergistic projects and to freely exchange tools, algorithms and know-how with each other, across all labs, seniorities and levels of experience.

The Bioinformatics Hub at the HUPO 2016 World Congress in Taipei was highly successful in bringing together many researchers interested in computational proteomics and bioinformatics to discuss topics important in the field. The hub was open daily from 8:30 – 5:30 during the congress, and the on-line program dynamically updated hourly with ongoing activities. Some of the more prominent topics addressed included discussions over the HPP Data Interpretation Guidelines v2.1, The HPP 50 Missing Protein Challenge, the proposed JPR Bioinformatics/Computational Resources Special Issue, use of preprint servers for computational proteomics manuscripts, MissingProteinPedia, privacy implications of proteomics data, OmicsDI, glycoproteomics informatics, quality control formats, and proteogenomics data file formats. Work on these topics will proceed based on these discussions, and we look forward to another exciting Bioinformatics Hub at next year's HUPO World Congress. See the Bioinformatics Hub web site for more information: https://github.com/CompMS/Overview/wiki/HUPO-2016

-Written by Eric Deutsch, Yves Vandenbrouck and Lennart Martens

C-HPP publishes 4th annual Special Issue in the Journal of Proteome Research

Fri, 04 Nov 2016 17:00:00 GMT

HUPO Chromosome-Centric Human Proteome Project (C-HPP) has recently published its 4th Special Issue of the Journal of Proteome Research (http://pubs.acs.org/toc/jprobs/15/11) which carries a total of 18 papers. This special issue highlights the progress on the C-HPP and its related projects in many aspects such as HPP Mass Spectrometry Data Interpretation Guidelines, 2016 HPP Metrics, Discovery of 267 Missing Proteins (currently 2930 proteins) and other biological aspects of newly identified proteins encoded by human chromosomes.

University of Victoria Genome British Columbia Proteomics Centre Partners with CPTAC

Thu, 29 Sep 2016 18:27:35 GMT

“We are delighted to be part of this CPTAC initiative and to be able to contribute to this important project. The University of Victoria-Genome BC Proteomics Centre will continue to develop MRM assays according to the CPTAC guidelines and upload them to the CPTAC portal. In addition, we intend to further develop these CPTAC MRM assays as validated kits to facilitate their use by the broader scientific community.” – Dr. Christoph Borchers, Ph.D., Director of the University of Victoria Genome BC Proteomics Centre, Canada

“We are excited to align forces with Christoph to provide open source, highly characterized, targeted MS assays to the community. The ability to reliably quantify proteins is a critical next step towards making the genome actionable and improving our understanding, diagnosis, and treatment of diseases. ” – Dr. Amanda Paulovich, Member of the Fred Hutchinson Cancer Research Center and co-Chair of the CPTAC Assay Development Working Group

“This generous contribution and future commitment by Christoph at the University of Victoria Genome British Columbia Proteomics Centre to deposit well-characterized, targeted MS assays into CPTAC’s Community Assay Portal which employ an experimental/analytical fit-for-purpose approach, will accelerate the evolution from genomics to proteomics.” – Dr. Henry Rodriguez, Director of the Office of Cancer Clinical Proteomics Research at the National Cancer Institute, National Institutes of Health

The below press release was sent by the NCI Office of Cancer Clinical Proteomics Research on August 29, 2016.

University of Victoria Genome British Columbia Proteomics Centre, a leader in proteomic technology development, has partnered with the U.S. National Cancer Institute (NCI) to make targeted proteomic assays accessible to the community through NCI’s CPTAC Assay Portal (https://assays.cancer.gov).

A key aspect of the Assay Portal is to provide space where national and international proteomics researchers from across the globe can upload and share their quantitative assays with standard operating procedures and guidelines. To meet this goal, NCI is continuing to improve the assay upload process to have an independent process for public/non-CPTAC teams to upload their assays in a seamless fashion and will provide update on this effort to the community as it comes available.

Targeted proteomic assays eliminate issues that are commonly observed using conventional protein detection systems (e.g. Western blotting), which are semi-quantitative at best, not readily multiplexed, and often non-specific. Until recently, non-standardized information for hundreds of targeted mass spectrometry-based assays was distributed across published journal articles. The CPTAC assay portal serves as a centralized public repository of highly characterized targeted MS assays, including standard operating protocols, reagents, and assay characterization data.

Dr. Christoph Borchers, Ph.D., Director of the University of Victoria Genome BC Proteomics Centre, Canada, has volunteered to be the first non-CPTAC researcher to upload targeted mass spectrometry-based assays to the portal. These multiple reaction monitoring (MRM-MS)-based assays fully adhere to the standards and guidelines developed by CPTAC and meet the minimum characterization requirements for entry to the portal, including development of multipoint response curve and repeatability assessment. In the portal landing page, which is designed to be relevant to biologists, researchers will be able to search for the Proteomics Centre assays by querying using the “non-CPTAC” term. Dr. Borchers has contributed 107 MRM assays to the portal in this initial phase, and is working on completing up to 2,000 assays that will be ultimately imported to the CPTAC Assay Portal.

“We are delighted to be working with the CPTAC on this important project,” says Dr. Borchers. “Standardization of protein quantitation is essential if mass spectrometry-based proteomics is going to be used for clinical assays. To assist in cancer-related research, we are planning to greatly extend the range of our MRM based assays in CPTAC to include assays for mouse proteins. The mouse is the preferred animal model for studying cancer, and will become even more important through the new CRISPR/Cas9 technology, which greatly facilitates the research of genetic mutations of cancer-related proteins in mice at a low cost.”

Dr. Amanda Paulovich, a Member of the Fred Hutchinson Cancer Research Center and co-Chair of the CPTAC Assay Development Working Group, notes that, “We are excited to take this important first step in opening up the Assay Portal for contributions from the entire community, bringing us one step closer to the goal of standardizing quantification of all proteins across the community to improve analytical rigor and reproducibility in protein-based research.”

Background
To empower researchers and democratize protein measurements, NCI launched the proteomics Assay Portal in 2014. This community web-based repository for well-characterized quantitative proteomic assays which was highlighted in a landmark paper in Nature Methods currently consists of greater than 900 targeted assays and serves as a public resource of methodologies and data related to cancer associated targets. By incorporating guidelines for assay characterization, the CPTAC Assay Portal takes a leap forward in enabling researchers to assess the performance of each assay as well as downloading all the data and information for implementing the assays. The ultimate goal is to standardize protein quantification and harmonize results across laboratories, improving our ability to validate molecular signatures and the reproducibility of preclinical research, as well as facilitating the regulatory approval of new drugs and diagnostics.

The Assay Portal also represents the application of “best practices” for targeted mass spectrometry developed during a two day-workshop held at the National Institutes of Health and published in 2014 in the journal of Molecular and Cellular Proteomics. In this workshop CPTAC, with input from the outside community that included the U.S. Food and Drug Administration and American Association for Clinical Chemistry, established a framework for MRM assay ‘fit-for purpose’ validation by defining three tiers of assays distinguished by their performance and extent of analytical characterization. Assays presented on the CPTAC portal predominantly represent ‘Tier 2’ assays, as described in the workshop report.

———————–
THE POWER OF RESEARCH COLLABORATION
About the University of Victoria Genome British Columbia Proteomics Centre
The University of Victoria Genome BC Proteomics Centre is a state-of-the-art proteomics research facility located at the University of Victoria’s Vancouver Island Technology Park in Victoria, British Columbia, Canada. Supported by Genome Canada, Genome BC and the University of Victoria, the Centre is the best-equipped proteomics research facility in Canada, with $10 million worth of specialized equipment including 16 mass spectrometers. The Centre is a not-for-profit facility that operates on a cost recovery model. It is the longest operating proteomics core facility in Canada, having been in operation since 1982, and serves clients in academia, industry and government on a fee-for-service and collaborative basis.

About National Cancer Institute’s CPTAC
The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis technologies (proteogenomics) to different cancer types. CPTAC is composed of expertise in proteomics, genomics, cancer biology, oncology and clinical chemistry, while creating open community resources that are widely used by the cancer community. For further information about CPTAC, go to http://proteomics.cancer.gov.

2016 HUPO Council Election - the results are in!

Tue, 20 Sep 2016 01:00:00 GMT

The 2016 HUPO Council Election results were announced at the General Assembly of Members on September 19, 2016 in Taipei during HUPO 2016. Council terms are three years and will extend from January 2017 to December 2019. We are pleased to congratulate the following future HUPO councilors.

Eastern Region

Yasushi Ishihama (Japan)

Terence Poon (Macau)

Anthony Purcell (Australia)

Central Region

Bernd Wollscheid (Switzerland)

Martin Larsen (Denmark)

Emma Lundberg (Sweden)

Western Region

Ileana Cristea (USA)

Benjamin Garcia (USA)

Aleksandra Nita-Lazar (USA)

Susan Weintraub (USA)

Diversity Representatives Appointed by Council and Confirmed by Electorate

Sanjeeva Srivastava (India)

Jong Shin Yoo (South Korea)

Ruth Birner-Grünberger (Austria)

Andrea Urbani (Italy)

Gilberto Domont (Brazil)

2017 HUPO Executive Committee Announced

Mon, 19 Sep 2016 01:00:00 GMT

Four future HUPO Executive Committee positions (for 2-year terms, starting January 2017) were elected during the HUPO Council Meeting on Sunday, September 18.

We are pleased to announce the following future HUPO Executive Committee members.

HUPO Secretary General – Emma Lundberg, Sweden

HUPO Treasurer – Peter Hoffmann, Australia

HUPO Member-at-Large – Lennart Martens, Belgium

HUPO Member-at-Large – Christopher Overall, Canada

B/D-HPP Newsletter

Mon, 12 Sep 2016 18:16:27 GMT

Welcome to the first BD-HPP newsletter!

Read the Newsletter Online

This communication is design to inform and encourage collaborative efforts within the HUPO community, within B/D-HPP initiatives as well as across B/D-HPP and C-HPP. In each issue, we aim to highlight the activities and achievements of two B/D-HPP initiatives, and celebrate a success story. The newsletter editor is Michelle Hill, a new HUPO council member from Brisbane, Australia.

In This Issue:

Welcome
HUPO 2016
Connecting with C-HPP
Translational Success Story – Bruker MALDI biotyper
Spotlights on B/D-HPP Initiatives:
Human Brain Proteome Project
Food and Nutrition Proteomics

Q3 HUPOST - September 2016

Sat, 10 Sep 2016 18:22:41 GMT

Q3 HUPOST – September 2016

Read the latest issue of the HUPOST online here.

ECR MANUSCRIPT COMPETITION – Finalists announced!

Sat, 10 Sep 2016 17:49:26 GMT

We are pleased to announce the three finalists of the Early Career Researcher (ECR) Manuscript Competition. The winner of the competition will be determined during the ECR Manuscript Competition session at HUPO 2016 in Taipei. The session takes place on September 21, from 09:30-10:15, in Room 102.

Cheng-Kang Chiang

Cheng-Kang Chiang is currently pursuing his postdoctoral training under Dr. Figeys supervision at University of Ottawa, Ottawa Institute of Systems Biology (OISB), Canada. He obtained his PhD from the Department of Chemistry, National Taiwan University with Dr. Huan-Tsung Chang. His current research interests include using quantitative mass spectrometric methodology to characterize and understand the cellular mechanisms of the circadian clock underlying environmental factors in metabolic processes, as well as deciphering key regulators between gut microbiota and host proteome at the mucosa-luminal interface of new-onset pediatric IBD patients.

Stefan J. Kempf

The aim of this study was to elucidate the effect of chronic low-dose-rate radiation exposure (1 mGy/day or 20 mGy/day – corresponding to doses of daily computed tomography (CT) scans) given over 300 days on the murine Apoe-/- hippocampus. Marked alteration in the phosphoproteome was found at both dose rates whereas changes in the unmodified and sialylated N-linked glycoproteins were scarce. The phosphoproteins were associated with control of synaptic plasticity, calcium-dependent signalling and brain metabolism. A reduced memory-related CREB signalling was found at both dose rates whereas synaptic morphology-related Rac1-Cofilin signalling was altered only at the lower dose rate. Adult neurogenesis, investigated by Ki67, GFAP and NeuN staining, and cell death (activated caspase-3) were not influenced at any dose or dose rate. This study shows that several molecular targets induced by chronic low-dose-rate radiation overlap with those of Alzheimer´s pathology that may suggest it as a contributing risk factor to this neurodegenerative disease.

Hannes Röst

I am a bioinformatics researcher interested in high-throughput technologies that allow us to study the molecular phenotype of a biological system comprehensively. I have worked on theoretical questions in targeted proteomics, contributed to the development of SWATH-MS and wrote the first software capable of targeted analysis of SWATH-MS data in high throughput. I studied at ETH Zurich, Switzerland, worked with Ruedi Aebersold during my PhD and I am now working with Mike Snyder at Stanford University to apply mass spectrometry in a personalized medicine context.

Stanford Medicine | Human Personal Omics Profiling

Fri, 19 Aug 2016 18:53:07 GMT

Mike Snyder’s lab at Stanford is leading the hPOP project. Please contact Sara Ahadi at sahadi(at)stanford.edu if you have any questions.

For more information visit http://med.stanford.edu/hpop.html

HPP Clinical Scientist Travel Grants Announced

Thu, 18 Aug 2016 18:54:37 GMT

We are pleased to congratulate the winners of the 2016 HPP Clinical Scientist Travel Grants!

Peter Bergsten, Sweden
Michael Chen, Canada
David Herrington, USA
Ana Konvalinka, Canada
Vinayak Nagaraja, Australia
Zhiwei Qiao, Japan

“Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome”

Mon, 15 Aug 2016 18:55:35 GMT

HUPO congratulates colleagues in the Moritz (Institute for Systems Biology) and the Aebersold (ETH Zurich) labs for their pivotal recent Cell paper “Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome” reported by Dr Ulrike Kusebauch

http://authors.elsevier.com/a/1TSJnL7PXN3iC – for free access until Sept 19, 2016.

In this remarkable work, the authors describe how the SRMAtlas provides definitive verified high-resolution spectra and multiplexed SRM assay coordinates and chromatographic peaks that identify 166,174 proteotypic peptides providing multiple, independent assays to quantify any human protein and numerous spliced variants, non-synonymous mutations, and post-translational modifications. SRMAtlas data are freely accessible as a resource at http://www.srmatlas.org/ and the paper demonstrates the SRMAtlas’ utility by examining protein network responses to (i) inhibition of cholesterol synthesis, and (ii) docetaxel sensitivity. HUPO applauds the SRMAtlas triumph as this supports proteome-wide quantification, as well as novel biology and disease hypothesis-driven research. The SRMAtlas demonstrates that the road to understanding the complete Human Proteome is progressing full-steam ahead, despite a few intricacies, challenges and blind alleys.

https://www.systemsbiology.org/research/quantitating-complete-human-proteome/

HUPO forecasts the completion of the Human Proteome Project (HPP) requires: (i) high-quality, publicly available evidence for every expressed protein from the human genome; (ii) analyses of the various forms these proteins take; (iii) spatiotemporal cellular and tissue localization; (iv) protein interaction and structural biology data; (v) an understanding of the biology of proteins and their many isoforms; and (vi) detailed information about their quantitation and roles in human wellness and disease. This journey must be based upon freely accessible resources containing high-quality, communally-verified “big data”, so that we can navigate the proteome’s complexity. Revised 2016 Human Proteome Project metrics and guidelines are anticipated to be released soon.

https://www.hupo.org/human-proteome-project/

APOLLO – proteogenomically zeroing in on cancer

Mon, 11 Jul 2016 18:58:43 GMT

July 11, 2016 — In the spirit of collaboration inspired by the Vice President’s Cancer Moonshot, the U.S. Department of Veterans Affairs (VA), the U.S. Department of Defense (DoD), and the U.S. National Cancer Institute (NCI) are proud to announce a new tri-agency coalition that will help cancer patients by enabling their oncologists to more rapidly and accurately identify effective drugs to treat cancer based on a patient’s unique proteogenomic profile.

The APOLLO Network — Applied Proteogenomics Organizational Learning and Outcomes — will look at both a patient’s genes (genomic analysis) and the expression of these genes in the form of proteins (proteomic analysis) to create the nation’s first system in which cancer patients are routinely screened for genomic abnormalities and proteomic information to match their tumor types to targeted therapies. Initially, APOLLO is focusing on a combined cohort of 8,000 cancer patients within the nation’s two largest healthcare systems — the VA and DoD — with the aim of expanding the program to additional cancer types and making findings available to physicians across the country. APOLLO is starting with lung cancer to address the pressing need of treating a form of cancer that is pervasive and prevalent among about veterans and service members. Approximately 8,000 veterans are diagnosed with lung cancer each year in the VA’s Veterans Health System alone.

The collaboration brings together the scientific and technical capabilities and facilities in DoD’s Murtha Cancer Center, the VA’s Veterans Health System, and the NCI’s Clinical Proteomic Tumor Analysis Consortium. Spurred by the NCI, genomics has launched a revolution in precision oncology by identifying targetable mutations in cancers. Unfortunately, there is still key missing biology when trying to reliably predict which patients’ tumors respond to any given therapy. This is likely because molecular drivers of cancer are derived not just from DNA, but also from proteins. Knowing more about a patient’s proteins should enable us to better predict how cancer will respond to a specific, targeted chemotherapy or combination therapy. A critical next step in the evolution of precision oncology is to continue to study what we are just learning in proteogenomics to identify the protein pathways and gene mutations in a tumor that drive cancer growth that can be vital to selecting targeted therapies more precisely. This is an exciting time for the field of proteogenomics. APOLLO Network will provide insight on the success of moving into the field of proteogenomics as a meaningful way to treat lung cancer patients with the promise of being able to quickly extend into other cancer types if proven to be successful.

The -omics approach reveals a key to the problem of child malnutrition

Mon, 04 Jul 2016 20:16:38 GMT

An interview with Professor Richard D. Semba, Johns Hopkins University

Interview conducted by Marta González-Freire, Ph.D., Visiting Fellow, National Institute on Aging, and early career scientist working on skeletal muscle proteomics with Dr. Luigi Ferrucci, Scientific Director of the National Institute on Aging.

Professor Richard D. Semba and Marta González-Freire, Ph.D

González-Freire: You have been a faculty member at the Johns Hopkins School of Medicine for your entire career. Your lab group was mostly focused on nutrition and immunology but you recently made a mid-career transition to proteomics and metabolomics. What happened?

SEMBA: My lab was doing conventional immunology and nutritional biochemistry using conventional platforms such as ELISA, HPLC, and atomic absorption spectrometry. I would call this “normal science”, which by nature, is largely corroborative. The research was mostly validation of single biomarkers in large study cohorts of older adults. I became restless. Normal science offered little in terms of discovery and generating new hypotheses. Recent advances in proteomics, metabolomics, and mass spectrometry certainly caught my attention.

González-Freire: How did you get started in proteomics?

SEMBA: Your mentor, Dr. Ferrucci, introduced me to Jennifer Van Eyk. He urged me to try something different. I soon found myself back at the bench in Jenny’s lab to learn sample preparation for proteomics. Jenny’s enthusiasm, teaching, and guidance were a life-changing experience. She recommended that I take the intensive summer course in proteomics at Cold Spring Harbor Laboratories. This influential course, run by Ileana Cristea and her colleagues, has launched the careers of many scientists in proteomics. And now Ileana has become a dear friend and collaborator.

González-Freire: Did the promise of the field meet your expectations?

SEMBA: Wow, maybe way beyond my expectations.

González-Freire: Were there any surprises?

SEMBA: Dealing with the sheer amount of data is a daunting challenge. The buzz in the field seems to center around detecting more and more proteins, but making sense of the biology compels one to read hundreds of papers. That is the bottleneck of the process.

González-Freire: I notice your research interests include eye research, aging, nutrition in developing countries, and history of medicine. How did you end up working so broadly?

SEMBA: I have academic attention deficit syndrome [laughing]. Somehow it all seems related to me. After my residency in ophthalmology, I worked in Indonesia on vitamin A deficiency, the leading cause of blindness in children. That links eye research with nutrition. Then I got interested in the relationship of micronutrient malnutrition with HIV/AIDS, so I worked many years in Malawi and Uganda doing clinical trials. In the meantime, I built up a nutritional biochemistry lab at Hopkins. I wanted to do more hypothesis-generating work, so I closed my work in Africa and started working on aging. The history of medicine relates to everything. I think scientists working in proteomics need to know J. J. Thomson, Francis Aston, and Dorothy Hodgkin.

González-Freire: What are your big projects right now?

SEMBA: We are using selected reaction monitoring (SRM) to characterize the relationship of the systemic complement pathway with age-related macular degeneration. Another application of SRM is to understand circulating proteoforms that are purportedly associated with aging, such as GDF8 and GDF11 and their circulating inhibitors. SRM should clarify the issue, since antibody and aptamer-based studies have yielded conflicting data.

González-Freire: How do you think proteomics and metabolomics can contribute to global health?

SEMBA: The work we just did on essential amino acids and child stunting overturned the widespread belief that children in developing countries receive adequate dietary protein. Children need quality protein in their diet, such as animal source foods. These results are already having an impact on approaches to child malnutrition.

González-Freire: How do you think we can use proteomics to understand aging?

SEMBA: Your GESTALT project at the National Institute on Aging is really important. You and Luigi are characterizing normative data on the proteome of many tissues, including skeletal muscle, across a wide age range of healthy individuals. This study will likely become the benchmark for proteomics in aging research.

González-Freire: Who have been the most influential people in your career?

SEMBA: The evolutionary biologist Charles Sibley played an important role in forming my own perspective on science. He had an ambitious project to construct the global phylogeny of birds using DNA. I worked for him as an undergraduate, helping him prepare a book. Then he sent me out to do fieldwork for a year in the Amazon in Peru and in the rainforests of Borneo – it was a rare experience. Our field team discovered three new species of birds to science: a hummingbird, a flycatcher, and a new genus of owl. The other influential scientist was Linda Fried, the expert on frailty and aging. We worked together for several years until she left to become dean at Columbia.

González-Freire: What do you view as the ideal laboratory?

SEMBA: Perhaps there is no such thing as the ideal laboratory. It depends on what you want to accomplish. My main focus is on the research, as I don’t have a large training program with dozens of graduate students and post-docs. I think clearly delineated research goals, a realistic lab schedule, clear communication, emphasis on papers and productivity, and investment in the career development of the people in your lab are paramount.

González-Freire: What do you do to relax?

SEMBA: I enjoy cooking for my friends. Food is sharing, sensory, symbolic, rich in social meaning, and forms the bond and social glue of our existence. I enjoy sharing meals and my cooking with friends from all walks of life. I swim about an hour every day. One of my biggest joys is classical piano. My favorites are Bach, Mozart, and Brahms.

González-Freire: What kind of advice would you give to younger scientists that are forming their careers?

SEMBA: Develop writing skills, a love of writing, and set ambitious goals to write and publish as many papers as possible. No paper is ever perfect, so don’t let perceived imperfection slow you down. Don’t procrastinate. Communicate clearly with your colleagues and mentors. Be responsive. Understand the history of your subject, as scientific disciplines and topics have their own trajectories. Luckily for you, the fields of proteomics and metabolomics are on the ascending trajectory, which promises a stimulating and productive career ahead of you.

Proteins with essential amino acids may be key to eliminating child nutrition in developing countries

Mon, 04 Jul 2016 20:00:00 GMT

Yu-Ju Chen, Academia Sinica, Taiwan

While proteins are widely recognized as playing key roles in nearly all processes in living organisms, an odd debate arose about the role of protein in the diet of malnourished children in developing countries.

Stunting affects about one-quarter of children under five years of age worldwide; the World Health Organization estimates that 156 million children were stunted in 2015, nearly all of whom live in low-income countries. Stunted growth is closely linked with impaired brain and organ growth and higher risks for obesity, diabetes and other chronic diseases later in adulthood. In the 1950s and 1960s, protein-rich food mixtures were the main focus of study as a treatment for malnutrition in children in developing countries. In 1974, a paper “The Great Protein Fiasco” published in The Lancet cast doubt upon the central role of protein in childhood malnutrition. The focus in the international nutrition community shifted from proteins to micronutrient malnutrition, that is, lack of vitamins and minerals for the following four decades.

A recent study of essential amino acids and child stunting challenged the widespread belief that children in developing countries receive adequate dietary protein. The work led by Richard Semba from Johns Hopkins University was published in the April 2016 issue of the journal EBioMedicine. Semba and colleagues applied a targeted MRM-mass spectrometry-based metabolomics approach to measure serum levels of amino acids, as well as other essential compounds including glycerophospholipids, sphingolipids and other metabolites in blood samples from a community-based study of more than 300 children ages 1 to 5 years, more than 60 percent of whom had stunted growth, from six villages in rural southern Malawi. Participants’ height and weight were recorded by trained field workers. The main finding is that children with stunting had lower serum concentrations of all nine essential amino acids (tryptophan, isoleucine, leucine, valine, methionine, threonine, histidine, phenylalanine, lysine) compared with nonstunted children. In addition, stunted children had 10 to 40 percent lower concentrations of other nutritional markers, such as conditionally essential amino acids (arginine, glycine, glutamine), nonessential amino acids (asparagine, glutamate, serine) and six different sphingolipids, which are essential ingredients for development of the brain. Stunting was also associated with alterations in serum glycerophospholipid concentrations.

Essential amino acids cannot be synthesized by the body. The richest sources of essential amino acids are animal-source foods, such as milk, eggs, and meat, and also soybeans. This study suggested that children need quality protein in their diet for normal growth. These results are stimulating new recommendations and approaches to child malnutrition. Semba and his colleagues hope that this research will prompt a broader discussion on how to address child malnutrition.

“Providing high-quality protein with sufficient levels of essential amino acids in developing countries will be a major challenge and will require substantial investment in the agricultural sector,” says Semba (quoted from press release of John Hopkins University, February 23, 2016).

This study challenges a long held paradigm about dietary protein for children in developing countries. Future studies are needed to address how lack of essential amino acids affects biological pathways and contributes to the pathogenesis of child stunting. Let’s look forwards to more discoveries from the proteomic community.

Dr. Lacey LaGrone and Malawi health workers measuring the length of a child at a rural health center.
Photo credit: Indi Trehan

Child Stunting is Associated with Low Circulating Essential Amino Acids (2016). EBioMedicine 6, 246–252. http://www.ebiomedicine.com/article/S2352-3964%2816%2930069-X/fulltext

Slate of candidates announced – HUPO Council Elections 2016

Fri, 01 Jul 2016 05:03:12 GMT

Dear HUPO Members,

The Nominations and Elections Committee of the Human Proteome Organization is pleased to announce the official slate of candidates for the HUPO Board of Directions (HUPO Council) election. HUPO wishes to express thanks to those candidates who are willing to stand for council election for a three-year term beginning in 2017 (2017-2019).

The election period for HUPO Council is August 26-September 18. Again this year, the vote is conducted online. All active HUPO members will receive an email containing a secure election ID code. Electors simply click on the link provided and cast their anonymous votes. Election IDs will be emailed to all active HUPO members on August 25, 2016. If you join as a member after this date you will given an election ID.

HUPO 2016 Slate of Candidates

Central Region Candidates – click here
Eastern Region Candidates – click here
Western Region Candidates – click here
Diversity Candidates – click here

2016 HUPO Award Recipients

Fri, 01 Jul 2016 04:04:48 GMT

The Human Proteome Organization presents a number of distinguished awards annually at the World Congress. HUPO gratefully acknowledges the support of the Industrial Advisory Board, the Journal of Proteome Research (ACS Publications), and Elsevier as sponsors of three of these awards. The HUPO Executive Committee and the Awards Committee would like to thank all those who submitted nominations for the 2016 awards.

It is with great enthusiasm that we present the 2016 HUPO Award Winners! Please join us in congratulating these outstanding scientists on their accomplishments and contributions to the field of proteomics. The awards will be presented at HUPO 2016 in Taipei and the winners will present a talk during the congress award session.

Distinguished Achievement in Proteomic Sciences (sponsored by the Journal of Proteome Research)

Ralph Bradshaw, College of Medicine, University of California, Irvine, USA

Discovery in Proteomic Sciences

Michael MacCoss, School of Medicine, University of Washington, USA

Science and Technology Award (sponsored by the Industrial Advisory Board)

Bob Bateman, Waters Corporation, Wilmslow, UK

John Hoyes, Waters Corporation, Wilmslow, UK

Translational Proteomics Award (sponsored by Elsevier)

Joshua LaBaer, Biodesign Institute, Arizona State University, USA

HUPOST Vol. 6, Q2 | June 2016

Thu, 30 Jun 2016 19:00:15 GMT

Read the Q2 HUPOST here! Q2 HUPOST – June 2016

Want to contribute to a future newsletter? Please submit your information to the HUPO Office at office@hupo.org.

“Proteomics – Translating the Code of Life” – new documentary released!

Wed, 22 Jun 2016 19:06:55 GMT

Watch the documentary HERE

(https://www.youtube.com/watch?v=m4U9bcnGtg4&feature=youtu.be)

The completion of Human Genome Project was a major landmark achievement for the life sciences community. With genomics setting a foundation in the quest to uncover the mysteries of life and biology, what lies next? What are the prospects and challenges as we explore the post-genomic world?

Proteins and proteomics are central to connect genomes with phenotypes and biological function. Proteomics provides a veritable foundation to address whole systems, and uses a broad unbiased approach to decipher post-genomic biology.

This documentary portrays the journey of “Proteomics”, discusses its advancements, achievements and key issues that lay ahead. The first section of the documentary introduces the Post-genomic Era and establishes the necessity of proteomics. The second section focuses on development of various proteomic Technological Platforms and how persistent efforts of proteomics scientists have resulted in the First Draft of the Human Proteome.

Next Generation Tools involving Trans-Proteomic Pipeline, SWATH-MS and Skyline have added to the arsenal of targeted proteomics. The proteomics community can contribute immensely to functional biology and offer innovative solutions in life sciences. Sustained and committed efforts from global proteomics communities like the Human Proteome Organization (HUPO) has helped proteomics establish an undeniable international presence. This has helped define the broader theme of research directions, thus, “Translating the Code of Life”.

Documentary created by Dr. Sanjeeva Srivastava and IIT Bombay Team

(http://www.bio.iitb.ac.in/~sanjeeva/documentary/)

Clinical Proteomics receives impact factor of 3.476

Wed, 22 Jun 2016 18:09:17 GMT

In the newly announced journal Impact Factor last week, we are pleased to see Clinical Proteomics received its impressive initial Impact Factor of 3.476. This puts Clinical Proteomics as one of nine proteomics journals that currently have official Impact Factors. Clinical Proteomics has special emphasis on promoting novel scientific research in the field of translational proteomics. This vision is in harmony with the theme of Human Proteome Organization (HUPO). For this reason, there were no surprises to see that Clinical Proteomics and HUPO have long shared members and journal board meetings have often taken place during the annual HUPO congresses. The Editor-in-chief of the Journal, Dr. Daniel Chan, is a founding member of HUPO and the recipient of the inaugural HUPO Translational proteomics Award. The editorial team includes many HUPO members and leaders, including Mark Baker, Christoph Borchers, Bruno Domon, Samir Hanash, Fuchu He, Stanley Hefta, Jacob Kagan, Jashua LaBaer, Gilbert Omenn, Young-Ki Paik, Akhilesh Pandey, Peipei Ping, Henry Rodriguez, Richard Semba, Michael Siu, Richard Smith, Mike Snyder, Sudhir Srivastava, Jennifer van Eyk, Marc Wilkins, Hui Zhang, and many others. Clinical Proteomics welcomes manuscript contributions by HUPO members and Human Proteome Project (HPP) contributors.

“I am looking forward to working with you all at HUPO to promote clinical proteomics research and publications.” -Dr. Daniel Chan, Editor-in-chief, Clinical Proteomics

https://clinicalproteomicsjournal.biomedcentral.com/

Clinical Scientist Travel Grants – call for submission

Wed, 01 Jun 2016 16:30:00 GMT

Deadline: June 30, 2016

The HPP is reaching out to clinical scientists or clinicians who are using or consider using proteomics for their research projects. HPP is supporting six (6) clinical scientists with a travel grant to attend the 2016 HUPO World Congress in Taipei, Taiwan that will take place from September 18-22, 2016.

Travel grant recipients will receive USD $1,000 to offset travel and hotel costs in addition to complimentary congress registration.

To learn more about applying for an HPP Clinical Scientist Travel Grant visit this page.

C-HPP Newsletter no.5 now available!

Wed, 04 May 2016 19:25:58 GMT

C-HPP NEWSLETTER no.5

Click on the link above to see the C-HPP Newsletter (no.5). In this annual report you will see the various activities of the C-HPP consortium members, news on future meetings, and related publications.

HUPO ratifies neXtProt alignment with PeptideAtlas Mass Spectrometry Metrics for Human Proteome Project

Fri, 29 Apr 2016 19:31:23 GMT

neXtProt has announced in their February 2016 release that its metrics for assigning proteins as protein evidence 1 (PE1) as part of the Human Proteome Project now align with those proposed by PeptideAtlas in September 2015.

Our collaborators at neXtProt state:

Entries whose protein(s) existence is based on evidence at the transcript level (PE2), homology (PE3) or a prediction (gene model; PE4) were previously upgraded to evidence at the protein level (PE1) if the entry had (i) 2 proteotypic peptides 7 or 8 amino acids in length or (ii) 1 peptide at least 9 aa coming from mass spectrometry experiments in neXtProt. This rule has been made more stringent so as to be in sync with the PeptideAtlas/HPP criteria for validating proteins using mass spectrometry data (i.e., at least 2 proteotypic peptides 9 aa in length or more which differ in at least 1 amino acid and which are not overlapping) are now required for the protein evidence to be upgraded to PE1.

For more details click here.

Proteins at work – the fascinating world of proteomics

Fri, 15 Apr 2016 19:32:44 GMT

Watch the video HERE.

This video provides a glimpse at the fascinating world of proteomics research, the study of all proteins that form the basis for life.

The video was produced for the lab of prof. dr. Albert Heck at Utrecht University and the Netherlands Proteomics Centre.

Q&A: Mike Snyder on Data-Driven Personalized Medicine for All, Stanford’s iPOP Study

Fri, 05 Feb 2016 20:38:09 GMT

www.genomeweb.com

Q&A: Mike Snyder on Data-Driven Personalized Medicine for All, Stanford’s iPOP Study

Snyder’s new book, “Genomics and Personalized Medicine,” serves as a primer for patients and doctors, touching on topics from tailored cancer therapy to wearable devices.

Capture All and then Release only the De-N-Glycosylated Peptides for Glycoproteomics

Mon, 01 Feb 2016 20:41:43 GMT

News in Science | HUPOST Vol. 6, Q1 Feb 2016

Kay-Hooi Khoo, Academia Sinica, Taiwan

Among the post-translational modifications, mass spectrometry (MS) analysis of protein glycosylation remains the most challenging due to the diversity in glycosylation. However, the glyco-savvy proteomic community continues to report major technical advances in all aspects of glycomics and glycoproteomics, from sample preparation, data acquisition to informatics associated with data analysis. It is particularly welcoming to see an increasing awareness and readiness to tackle analysis of intact N-glycopeptides instead of only defining the occupied N-glycosylation sites by the easier route of analyzing the de-N-glycosylated peptides. In general, the few key enabling steps in any MS-based glycoproteomic attempt to map the site-specific glycosylation pattern include 1) enrichment of the glycopeptides; 2) construction of glycan and glycosite-containing peptide library or database to allow identification of the intact glycopeptides by any of the currently available search algorithm; 3) generation of sufficiently good quality glycopeptide MS/MS data in the first place, which usually requires the presence of peptide core fragment ions, peptide core+HexNAc or the Y1 ion, and high resolution/accurate mass MS1 data of the glycopeptide precursors.

The main innovation introduced by Hui Zhang’s group at Johns Hopkins University in a recent work published in the Jan 2016 issue of Nature Biotechnology is the way the N-glycan and N-glycosite containing peptide database was generated. Most other groups resorted to identifying as many of the PNGaseF-de-N-glycosylated peptides from analysis of a separate aliquot of the enriched glycopeptide fractions and use a publicly available glycan library such as the GlycomeDB, or the default library option available in commercial software such as Byonic. The authors took a different approach by modifying their long established hydrazide chemistry-based glycopeptide-specific capture method. Solid phase immobilization was accomplished non-selectively instead by conjugation to aldehyde-functionalized solid support via reaction with the N-termini of all tryptic peptides and, after de-N-glycosylation by PNGase F, Asp-N was used to selectively cleave and release only glycosite-containing peptides with Asp at at the initially N-glycosylated Asn site. Thus only peptides carrying N-glycosites will be selectively recovered and identified. This is a very clever approach although many chemistry modification steps are involved including modifying sequentially the e-amino group of Lys and free carboxylic groups of C-termini, Asp, Glu and sialic acids. The result is quite impressive and the authors showed that it led to many more N-glycosite-containing peptides identified. The authors also went on to profile the released glycans in order to construct their own sample-specific glycan library. This was performed by both MALDI- and LC-MS and facilitated by the sialic acids now being modified by aniline. For actual analysis of the intact glycopeptides, HILIC enriched glycopeptides were subjected to LC-HCD MS/MS on a Q-Exactive instrument and the resulting spectra searched against the custom derived database using the precursor mass-matching option of their in-house developed GPQuest software. With filtering based on the presence of peptide+HexNAc and/or peptide ions, as well as ≥7 observed b and y ions (1% FDR), this resulted in positive assignment of 4,562 oxonium ion-containing spectra to 1,562 unique glycopeptides containing 518 glycosites and 81 glycans from OVCAR-3 cells.

Key steps in solid phase extraction of N-glycans and N-glycosite containing peptides.
Image adapted by Dr. Kay-Hooi Khoo, Academia Sinica, Taiwan

Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides (2016) Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Hoti N, Zhang Z, Chan DW and Zhang H. Nat Biotechnol. 34, 84-88.

http://www.nature.com/nbt/journal/v34/n1/abs/nbt.3403.html

TPWIS Reflections 2015

Tue, 05 Jan 2016 20:45:13 GMT

Dear All,

Wishing you all Merry Christmas and Happy New Year-2016!

It brings us great pleasure to announce that the Targeted Proteomics Workshop and International Symposium (TPWIS-2015) followed by GIAN proteomics course ended on a high note. Overall 7 parallel events were conducted at IIT Bombay during 10th – 19th Dec 2015 for the unique set of participants in each event.

TPW – Targeted Proteomics Workshop (10-14 Dec 2015)
TPP – Trans-Proteomic Pipeline Workshop (10-14 Dec 2015)
HR-LC-MS Workshop (10-12 Dec 2015)
Targeted Proteomics International Symposium (13-14 Dec 2015)
Education Day (12 Dec 2015)
Innovative Seminars (10-12 Dec 2015)
GIAN Proteomics – Global Initiative of Academic Networks (10 – 19 Dec 2015)

We take this opportunity to thank all the distinguished speakers and invited guests for providing their valuable perspectives to the audience. This ambitious effort of organising dedicated workshops and symposium heavily benefitted large numbers of participants. We wish to extend our appreciation to all delegates for their active participation in this multi-faceted event.

Event photographs are now available online: http://www.bio.iitb.ac.in/~sanjeeva/itpws/award-winners/

We are humbled by the support you all have provided us and made it a very stimulating, enjoyable and one of the very unique international events of 2015. We hope that TPWIS-2015 has been as memorable to you, as it has been for us. The attached “Reflections” booklet (click here: TPWIS-2015_Reflections) is a memoir of the TPWIS-2015 and we wish that these remembrances and experience would last you a lifetime.

Happy holidays!
Warm regards,
Sanjeeva

Dr. Sanjeeva Srivastava
Convener, TPWIS-2015

New HPP Guidelines Established

Tue, 15 Dec 2015 20:48:41 GMT

The HPP aims to hold participants and authors to rigorous standards for publication and dissemination of results. All data are to be submitted to a ProteomeXchange public data repository, statistical analyses are to be performed to a high standard, and extraordinary claims of detection of “missing proteins” or novel coding elements require extraordinary evidence. The first set of guidelines was approved in 2012. Version 2.0.1 of the guidelines was approved in December 1, 2015. The newest guidelines should be applied to all contributions.

HPP Data Interpretation Guidelines version 2.0.1 (approved 2015-12-1):

The current version of HPP Data Interpretation Guidelines is version 2.0.1. Please apply these guidelines to all new HPP contributions. If errors are detected or slight amendments are made, the updated guidelines will be posted here. Therefore, please check back in this location for a final version before submitting your manuscript. A filled out checklist must be submitted with the manuscript for inspection by the editors and reviewers. Any non-adherence to the guidelines must be explained in the space provided on the form.

2015 HPP Data Interpretation Guidelines version 2.0.1 [PDF].

Important Note: If your manuscript is being submitted to JPR for the HPP special issue, the JPR guidelines also apply. In cases where the JPR guidelines and these HPP guidelines conflict, the HPP guidelines are more stringent in all cases and take precedence over the JPR guidelines. See the Current JPR Guidelines.

2012 Guidelines (deprecated): The 2012 HPP Guidelines were in effect for 3 years and are still mentioned here, but are now considered obsolete. Please apply the current guidelines to efforts for new contributions.

Version 1.0 of the HPP Guidelines, now obsolete.

New version of the human protein atlas

Sun, 06 Dec 2015 20:54:15 GMT

STOCKHOLM, Sweden – 16 October, 2015

The Human Protein Atlas today launched a new version of the database. The major new additions to version 14 are a new Mouse Brain Atlas and a new approach for antibody validation.

The Human Protein Atlas, a major multinational research project supported by the Knut and Alice Wallenberg Foundation, today launched a new version of the database. Since the release of version 13 at end of 2014, new data has been added and the atlas now holds data on more than 25 000 antibodies, covering over 17 000 of the human genes (approximately 86% of the human genome). Focus for this release has been to improve validation of the antibodies used to map the human proteome and the inclusion a new atlas; the Mouse Brain Atlas, created by the Fluorescence Tissue Profiling facility at Science for Life Laboratory (SciLifeLab) in Stockholm.

The current version of the human protein atlas holds a comprehensive map of protein expression patterns in normal human tissues down to the single cell level. To assure the correct interpretation of the data, the RNA-seq data from transcriptomics has been evaluated against the gene/protein characterization data retrieved from antibody-based methods; antibody reliability, sub-optimal experimental procedures, and potential cross-reactivity has been assessed. The result of the extensive evaluation is summarized in a data reliability description. Currently, almost 7500 genes have been updated with this knowledge-based annotation. In addition to this, co-localization of a fluorescent protein with the target protein has been introduced for antibody characterization, and complements the previously introduced gene silencing (siRNA) technique. In total, 104 genes have been analyzed using co-localization, 256 genes have been silenced and analyzed using immunocytochemistry, and 190 genes have been silenced and analyzed using western blot.

Many of the mouse proteins have extensive homology with the human counterpart and this forms the basis for using the mouse brain as a model for the corresponding human brain to explore the expression and distribution of proteins in the various regions and cells of the brain. The new Mouse Brain Atlas, introduced in this version, includes additional brain regions and has additional information on cellular and sub cellular distribution of proteins in the brain. Currently, 88 genes and 129 brain regions are covered in the Mouse Brain Atlas.

“We believe this antibody-based data set is a valuable complement to our own human protein atlas and other international efforts that map the building-blocks of the brain, such as the Allen Brain Atlas and the Gensat effort.” says Dr Jan Mulder, head of the Mouse Brain Atlas effort at SciLifeLab. The atlas is interactive, with the possibility of zooming in from a full brain section to single cells in a specific region of the brain.

About the Human Protein Atlas project

The Human Protein Atlas project, funded by the Knut and Alice Wallenberg Foundation, has been set up to allow for a systematic exploration of the human proteome using antibody-based proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main sites are located at AlbaNova and SciLifeLab, KTH – Royal Institute of Technology, Stockholm, Sweden, and the Rudbeck Laboratory, Uppsala University, Uppsala, Sweden. For more information on the Human Protein Atlas, visit our website at www.proteinatlas.org.

NEWS IN SCIENCE | HUPOST Vol. 5, Q4, Nov 2015

Mon, 30 Nov 2015 21:22:34 GMT

By Chia-Feng Tsai & Yasushi Ishihama, Kyoto University

Dysregulation of cellular signaling based on protein phosphorylation is closely linked to pathogenesis of human diseases and therapeutic strategies to control the phospho-signaling have been accepted to develop molecular-targeting drugs for cancer. MS-based quantitative phosphoproteomic approaches have been widely used to quantify over 10,000 phosphorylation sites by utilizing strong cation exchange chromatography, hydrophilic interaction chromatography or basic-pH reversed-phase chromatography to fractionate the complex samples. However, such extensive fractionation approaches require longer LC-MS measurement time as well as tedious pretreatment steps, resulting in reduced throughput and low reproducibility. Besides, these approaches cannot be applied to primary cells of rare tissues or clinical biopsy samples due to the limited starting materials.

To address these issues, Humphrey et al. (from Matthias Mann’s group) at Max Planck Institute of Biochemistry have developed a streamlined phosphoproteomics workflow called “EasyPhos” which has been designed as a high throughput and simplified workflow to study time-resolved phosphorylation alteration in vivo without any pre-fractionation strategy. They used trifluoroethanol for the digestion buffer which allows bypassing the peptide desalting step before phosphopeptide enrichment. This protocol can reduce the potential sample loss during the desalting process implemented in the conventional protocols. Besides, this simplified procedure can be expanded to a 96-well plate format to increase the throughput of phosphopeptide enrichment. The combination of this workflow with Q Exactive benchtop Orbitrap mass spectrometer allows monitoring of more than 10,000 phosphorylation sites from a mouse cell line by single-shot LC-MS/MS analysis with 2hr gradient. The applicability of this parallelized EasyPhos workflow has been demonstrated on the analysis of liver phosphoproteomes at different time points (early and intermediate) in fasted mice under insulin exposure. Up to 31,605 phosphopeptides (25,507 phosphorylation sites belong to class 1) from 6,138 phosphoproteins were identified from 91 biologically distinct liver tissues by the high throughput 96-well EasyPhos assay. Importantly, at least six biological replicate analyses (separate mice) per sample for each time point provide a highly statistical power to illustrate time-resolved maps of insulin signaling. Moreover, these dynamics datasets illuminate not only the insulin-mediated signaling network but also the signaling cascade from cell surface to the nucleus within 1 min in vivo. This rapid and high throughput EasyPhos workflow will facilitate to accumulate the knowledges of cellular signaling dynamics under physiological or pathological regulation.

Figure reprinted with permission of the Nature Publishing Group

This study was reported in the journal of Nature Biotechnology on August 17, 2015.

Link: http://www.nature.com/nbt/journal/v33/n9/abs/nbt.3327.html

Prioritizing Proteomics Assay Development for Clinical Translation

Mon, 09 Nov 2015 20:57:26 GMT

Read the full article here: Prioritizing Proteomics Assay Development for Clinical Translation

Vol. 66, No. 2, 2015
Journal of the American College of Cardiology
© 2015 by the American College of Cardiology Foundation
Published by Elsevier Inc.

Priorities and trends in the study of proteins in eye research, 1924-2014

Mon, 09 Nov 2015 20:50:47 GMT

Richard D. Semba, Maggie Lam, Kai Sun, Pingbo Zhang, Debra A. Schaumberg, Luigi Ferrucci, Peipei Ping, and Jennifer E. Van Eyk

Read the full article here: Priorities and trends in the study of proteins in eye research, 1924-2014

www.clinical.proteomics-journal.com

Proteomics Clin. Appl. 2015, 00, 1-18

DOI 10.1002/prca.201500006

High-protein research | NATURE 2015

Mon, 09 Nov 2015 18:59:57 GMT

By Neil Savage

The effort to catalogue proteins goes deeper in a push to make genetics research deliver practical benefits.

Published in Nature: S6 | NATURE | VOL 527 | NOV 2015

For more background, read the Metrics for the Human Proteome Project 2015.

State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet

Tue, 08 Sep 2015 20:03:29 GMT

Read the full article here: State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

Tue, 08 Sep 2015 20:00:02 GMT

Read the full article here: JPR-Metrics for the Human Proteome Project 2015

Discovery of unexplored potential of lipid-binding proteome for ligand/drug development

Sat, 05 Sep 2015 20:25:21 GMT

Niphakis, M.J. et al. Cell 161, 1668–1680 (18 June 2015)
News in Science (HUPOST Vol. 5, Q3 September 2015)

Lipids are a class of hydrocarbon-containing natural molecules; important examples include some vitamins (A, D, E), hormones (estrogen, testosterone), neurotransmitters (endocannabinoids) and components of fat (triglycerides, cholesterol). Their biological functions to regulate cell physiology and disease are often mediated through interactions with proteins. Despite the fact that a substantial number of drug targets are lipid-binding proteins, it has been challenging to establish a global portrait of how lipids interact with proteins in cells.

Benjamin F. Cravatt’s team at The Scripps Research Institute (TSRI) has devised a powerful chemical proteomic method to map the human lipid-binding proteome. In this study, Niphakis and colleagues described a set of fatty acid–based chemical probes combined with quantitative mass spectrometry to provide the first global portrait of lipid-protein interactions in human cells. Their results revealed a surprisingly large number of lipid-protein interactions from diverse functional classes, including some interactions which are already targeted by existing drugs and, most importantly, many novel lipid-binding proteins. The probes can also be used to identify the targets of drugs that disrupt lipid-protein interactions in cells, pointing to the broad potential of lipid-binding proteins for ligand/drug development.

“Traditionally, scientists have theorized fairly narrow limits for the types of proteins that can be targeted with small-molecule ligands, but our results suggest that those boundaries are much wider,” said Cravatt (adapted from News Release of The Scripps Research Institute)

This study was reported in the journal of Cell on June 18, 2015.

Figure provided by Benjamin F. Cravatt

http://www.cell.com/cell/abstract/S0092-8674(15)00635-2

Human Proteome Organization (HUPO) News

Have you recently published an original article on proteomics research?

HUPOST February 2026

Submit your abstract and participate in the Poster Competition at HUPO 2026 in Singapore!

Overview and Evaluation of the HUPO 2025 ETC Pre-Congress Training Sessions

HUPO ECR Committee Webinar: Maximizing the Impact of your Abstract and Keywords

HUPOST January 2026

HUPO ECR Committee Welcomes New Members

Call for the 2026 HUPO Early Career Researcher Manuscript Competition!

HUPOST December 2025

HUPO ECR Poster Competition

Congratulations to the winner of the 3-Minute Thesis (3MT) Competition, Ruxandra Bighiu!

Congratulations to the winner of the HUPO 2025 ECR Manuscript Competition, Dr. Xiang Zheng!

Winner

Announcing the HUPO Award 2025 Winners!

HUPOST October 2025

HUPOST September 2025

Get Ready for the 3-Minute Thesis (3MT) Competition Final!

Meet HUPO 2025 ECR Manuscript Competition Finalist: Dr. Xiang Zheng!

Call for Nominations: HUPO EC - VICE PRESIDENT

HUPOST August 2025

Meet the finalist of the HUPO 2025 ECR Manuscript Competition: Dr. Julia Bubis!

4th annual Ubuntu Proteomics Summer School (UPSS)

Call for Nominations: HUPO Council

HUPOST July 2025

HUPO ECR Committee Welcomes a New Member

Meet HUPO 2025 ECR Manuscript Competition finalist: Dr. Arun Vadivel!

HUPOST June 2025

HUPOST May 2025

Applications are open for the HUPO Rising Star Award!

Join ECR Mentoring Sessions at the HUPO World Congress 2025

The ETC Committee welcomes its newest member, Dr. Sayantani Chatterjee

BD-HPP Presentation Q2 - SCI & Metaproteomics

HUPO ETC Webinar Series: Pathology, Proteomics and Precision Medicine - Prof. Ed. Nice

HUPOST April 2025

The 2025 HUPO ECR Poster Competition is still open for entries!

There’s still time! We’ve extended the deadline for the HUPO Early Career Researcher Manuscript Competition to May 4th, 2025

We’re looking for the next HUPO Rising Star!

31st C-HPP Symposium

HUPOST March 2025

Keep an eye out for the HUPO Rising Star Award

The 2025 HUPO ECR Poster Competition is open for entries!

Don’t miss your chance to apply for the 2025 HUPO Early Career Researcher Manuscript Competition!

6th InPPO Conference

HUPOST February 2025

30th Chromosome-Centric Human Proteome Project Workshop

29th Chromosome-Centric Human Proteome Project Workshop, 2024 Chromosome Team Anniversary

HUPO ECR Committee Welcomes New Members

Call for the 2025 HUPO Early Career Researcher Manuscript Competition!

HUPO ECR Events at HUPO 2025

HUPOST January 2025

HUPO Education and Training Committee: Pre-Congress Training Course Summary

The "Proteomics Essay Corner" is on. We have our first submission.

HUPOST December 2024

ECR Committee Welcomes New Leadership

HUPOST November 2024

3-Minute Thesis Competition: Big Ideas in a Short Time

A Lively HUPO 2024 Poster Competition

Early Career Researchers Put on a Show at the Manuscript Competition: Proteomics Highlight of the Year Session during HUPO 2024

Missed the Mentoring Sessions at HUPO? We Have You Covered!

ETC Webinar Series September 9th, 2024: Dr. Philip Remeš

Creation of the HPP Portal – A Knowledge Hub to Support the HPP Grand Challenge

Fun Under the African Sun - Ubuntu Proteomics Summer School

Introducing the Proteomics Essay Corner!

HUPOST October 2024

Spotlight on the Proteomics Highlights of the Year

Calling All Proteomics Contributors: ﻿Share your Story!

Notice of HUPO General Assembly of Members (GAM)

UniProt Actively Supporting the HPP Grand Challenge

Join the ECR Mentoring Sessions at HUPO 2024!

C-HPP Workshop Program

ECR is delighted to showcase the finalists of the 10th edition of the annual manuscript competition.

Meet the Finalists for the 2024 Poster Competition

HUPOST September 2024

Meet the 2024 Finalists for the 3-Minute Thesis Competition

ECR Delighted to Showcase the Finalists of the 10th Edition of the Annual Manuscript Competition

News from the HUPO Human Brain Proteome Project (HBPP)

HUPOST August 2024

ECR Delighted to Showcase the Finalists of the 10th Edition of the Annual Manuscript Competition﻿

News from C-HPP

Calling All Proteomics Contributors: Share your Story!

ECR Delighted to Showcase the Finalists of the 10th Edition of the Annual Manuscript Competition