NewS

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.

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

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:

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:

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: 

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)

• 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!

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!

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.

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:

Explore galleries from the 2023 and 2024 schools, view the YouTube 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