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Newsletter of the Human Proteome Organization

Current and past HUPOST issues are posted here for your review. Stories, highlights, news, and announcements are gladly accepted for inclusion in the HUPOST. Please submit your information to HUPO Office.

FEATURED ARTICLES


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  • 29 Nov 2021 5:58 AM | Anonymous member (Administrator)

    Written by Chris Overall, C-HPP Chair, Canada

    C-HPP Virtual Principal Investigators Meeting, November 12, 2021, the HPP day, HUPO ReConnect

    The election results were announced for the EC of the C-HPP. The new Co-Chair of the C-HPP will be Dr Je-Yoel Cho (2022-2024), who will replace Dr Young Ki Paik. Dr Cho is at the Seoul National University and is the Leader of the Chromosome 9 team. We look forward to his contributions and leadership in the next three years. Dr Je-Yoel Cho will join Lydie Lane (2021-2023) as Co-Chair and Chris Overall as Chair of the C-HPP (2022-2024).

    Another new face for the C-HPP EC member at large for 2022-2024 is Dr Gong Zhang from the Institute of Life and Health Engineering, Jinan University, China and who is also the new leader of the Chromosome 8 Team. Peter Horvatovich is again the Secretary General (2020-2022) and member at large, as is Gilberto Domont (2022-2024) and Chris Overall is the continuing Chair of the C-HPP.

    We were pleased to announce that a Danish team has joined the C-HPP with Dr Ulrich auf dem Keller, Technical University of Denmark (DTU) leading the new Danish Chromosome 21 team. Finally, Chromosome 22 has a new leader from a newly forming Israeli team, Dr Oded Kleifeld, Technion, Israel Institute of Technology.

    Tribute to Young-Ki Paik

    Dr Young-Ki Paik with Prof. Sam Hanash coordinated and pioneered the launch of HUPO, 20 years ago, at a time when many scientists did not even know what proteomics was. In particular, the HPP has been the flagship project of HUPO under his leadership and coordination.  As President of HUPO Young-Ki played a key role in initiating the C-HPP initiative and developing the concept of individual countries taking ownership of characterizing the protein coding genes in a selected chromosome. The concept allowed the development of a global initiative and facilitated funding of individual projects with a clear country ownership and a strong sense of local achievements.  Young-Ki was always superbly organized and strategic as illustrated by the publication in Nature biotechnology of two of the early papers defining the C-HPP initiative. He has made major contributions through his leadership, recruitment of team members, EC members, convening C-HPP workshops, hosting the C-HPP Portal, raising funding support through the Korean Government, and he has tirelessly participated as a Guest Editor of the JPR Special Issue every year. More recently, he was instrumental in his visionary project to functionalize proteins with no known or inferred function, the CP-50 initiative in the C-HPP. The importance of this concept is now being expanded as a new HPP-wide Grand Challenge to functionalise the entire human proteome. He has published extensively on the HPP, the C-HPP and his own results and data in finding MPs and uPE1s, and so much more, including being a personal inspiration. Throughout all these achievements, Young-Ki has expanded and guided the C-HPP and brought in new teams and leadership and nurtured their continuing growth and development of the C-HPP, all with humility and great modesty. He will be sorely missed. Enjoy your well-deserved retirement Young-Ki.

    neXT-MP50 and neXt-CP50 Reports

    The neXT-MP50 and neXt-CP50 Reports are posted on the C-HPP Portal and the C-HPP wiki.

    neXtProt Support

    neXt-Prot needs you! Without support the official database of the HPP will close in the next two tears. Become a sponsor or enter a service contract to assist your projects here. Please contact the Director of neXt-Prot, Dr Lydie Lane: lydie.lane(at)sb-sib.ch.

    The Journal of Proteome Research Special Issue on the Human Proteome Project

    Watch for the 9th Annual Special Issue on the HPP that will be published in the first few days of December. As a teaser, here is this year’s cover.


  • 26 Nov 2021 1:26 PM | Anonymous member (Administrator)

    Written by Emily Hashimoto-Roth, University of Ottawa, Canada

    The HUPO Early Career Researcher (ECR) Initiative hosted three mentoring sessions throughout the HUPO ReCONNECT 2021 Main Congress. These sessions covered a diverse array of topics with the hopes of engaging and informing trainees and early career researchers alike and featured influential speakers. 

    How to successfully balance a personal life while in academia (November 15, 2021)

    The mentoring sessions were kicked off with the ever-popular topic of maintaining a healthy work-life balance while in academia. This important session, which was chaired by Maurine Fucito (D'Annunzio University of Chieti–Pescara) and Dr. Blandine Chazarin (Cedars-Sinai Hospital), featured Dr. Christine Carapito (University of Strasbourg), Dr. Harry Whitwell (Imperial College London), and Dr. Jennifer Geddes-McAlister (University of Guelph), all of whom gave invaluable insights and advice on this challenging issue. The audience came with questions at-the-ready for the panel of mentors, from starting families as early career researchers to setting up boundaries to preserve one’s personal life (and not feeling guilty about it!).

    Scientific Integrity (November 17, 2021)

    The second mentoring session focused on scientific integrity. During this session, which was chaired by Andreas Hober (KTH Royal Institute of Technology) and Emily Hashimoto-Roth (University of Ottawa), early career researchers had the pleasure of listening to Dr. Suzanne Farley (PLOS), Dr. Anne-Claude Gingras (Lunenfeld-Tanenbaum Research Institute), and Dr. Stephen Pennington (University College Dublin), sharing their experiences from both the publishing and research perspectives. Their presentations were followed by an engaging discussion, highlighting the responsibilities the research community must uphold to prevent scientific misconduct and promote transparency throughout the entire research process.

    Getting started on writing manuscripts, grants, and fellowships (November 19, 2021)


    The nuances of writing in all its forms were covered in the final mentoring session sponsored by the Journal of Proteome Research and chaired by Dr. Mio Iwasaki (Kyoto University), Dr. Justyna Fert-Bober (Cedars-Sinai Heart Institute) and Dr. Robert Rivers (National Institutes of Health). Dr. Rebekah Gundry (University of Nebraska) and Dr. Yasushi Ishihama (Kyoto University) graced the audience with a plethora of advice for writing, proofreading, and critically assessing one’s writing pieces. These talks were only bolstered by Dr. Zhengzheng Zhang’s input, an editor at Molecular Omics. The audience came alive with questions and a quick poll at the end of the session revealed that attendees felt inspired to get writing!

  • 28 Jun 2021 3:26 PM | Anonymous

    This is your chance as an ECR to have your proteomics questions answered by experts in our field! Participating experts are Drs. Claire Eyers, Joshua Coon, Christoph Messner, Olly Crook, Helen Cooper, Maria Robles, Erwin Schoof, and Tami Geiger.

    All of us constantly have a number of questions running through our head, but it is not always easy to find someone to answer them. This session will allow you to ask experts in our field your proteomics related questions in an informal setting. If you are an ECR this “Meet-the-Expert” session is free of charge to you. A small number of spaces are available to ECRs who are not registered for the conference. Assignment of the limited available spaces is done based on the "first come, first serve" principle.

    Join us by registering @ https://forms.gle/AcvJDs2JhgZEvfnTA. More information @ https://www.bspr-interact.com/

  • 28 Jun 2021 1:26 PM | Anonymous

    The HUPO ECR Initiative is proud to welcome two new members in its organization: Maurine Fucito, a Ph.D. student at University G. D’Annunzio of Chieti-Pescara in Italy and Christian Moritz, a postdoctoral researcher at Universities of Lyon in France. Please click here to read more of these promising young researchers.

    Maurine Fucito is a Marie Skłodowska-Curie Fellow at the Center for Advanced Studies and Technology (CAST) at the University G. D’Annunzio of Chieti-Pescara, Italy. After four years at the University of Liège, Belgium and one year at the University of Aveiro, Portugal studying chemistry, she started her Ph.D. in February 2020. She is part of the PMSMatTrain project that aims at developing a novel biomaterial-based device for the treatment of progressive multiple sclerosis. Her work consists in analysing lipids and proteins alteration in multiple sclerosis like models using mass spectrometry (LC-MS/MS and MALDI-MS Imaging) to validate the therapeutic efficacy of this novel device and to better understand the disease pathophysiology. In December 2020, she became a core member of the Young Proteomics Investigators Club (YPIC), an enthusiastic group of young scientists supporting ECRs.

    Christian Moritz is a postdoctoral researcher at the Universities of Lyon and Saint-Étienne, France, as well as the Hospital of Saint-Etienne. 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 autoimmune-related diseases of the peripheral nervous system.

  • 28 Jun 2021 11:09 AM | Anonymous

    The HUPO Early Career Researcher (ECR) initiative is delighted to announce that once again this year it will hold its Poster Competition at HUPO Reconnect 2021 (November 15-19) thanks to the support of its sponsor: Molecular Omics.


    This year, for the first time, the competition will be open to all graduate students (Master’s and Ph.D.) Eight presenters will be selected based on the excellence of their abstracts to give a short oral presentation on their poster at HUPO Reconnect 2021. A panel of judges will select the best presentations given at the conference, $300 (1st place) and $150 (2nd and 3rd place). Click here for more details about how to enter the competition.

    The HUPO Early Career Researcher (ECR) initiative is delighted to announce that once again this year it will hold its Poster Competition at HUPO Reconnect 2021 (November 15-19) thanks to the support of its sponsor: Molecule Omics. This year, for the first time, the competition will be open to all graduate students (Master’s and Ph.D.) Eight presenters will be selected based on the excellence of their abstracts to give a short oral presentation on their poster at HUPO Reconnect 2021. A panel of judges will select the best presentations given at the conference, $300 (1st place) and $150 (2nd and 3rd place).

    How to enter:

    • Submit an abstract via the HUPO Reconnect 2021 abstract submission form 
    • Select to enter the graduate students Poster Competition when asked on the form.
    • Upload to the form the supporting documentation to confirm student status (e.g., student registration confirmation or letter from supervisor).
    • Send a short text (maximum five sentences) describing the main achievements of your work to ecr@hupo.org. Subject of your email should be: HUPO Reconnect 2021 graduate students Poster Competition – YOUR NAME
    • The presenting first author (or co-first author) must be a Graduate Student.

    Finalists will be notified before the end of September – beginning of October 2021.

    For queries on the competition please contact Chelsea Prangnell at chelsea@hupo.org

  • 28 May 2021 3:38 PM | Anonymous member (Administrator)

    Written by Eric Deutsch, Institute for Systems Biology USA; David L. Tabb, Pasteur Institute, Department of Structural Biology and Chemistry France; Sandra Orchard, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) UK; Juan Antonio Vizcaíno European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) UK; Andrew R Jones, Institute of Systems, Molecular and Integrative Biology UK

    The Proteomics Standards Initiative (PSI) was formed as a HUPO working group back in 2002, with an aim to improve data sharing and standardisation in proteomics. At that time, proteomics was a rapidly developing technique, and the concept of sharing data in support of publications was still in its infancy. Most proteomics articles reported tables of protein identifications or quantitative values in PDF format, inhibiting their import into other software. Visualizing peptide-spectrum matches was rare, preventing critical assessment of PSM quality. The PSI’s primary aims were i) to develop data standards that would enable the submission of data (raw and/or processed) to public databases or for interchange between software, improving transparency and data re-use; ii) to develop “reporting requirements” indicating the types of information that should be recorded e.g. in a Methods section or database entry, to allow critical interpretation of results; and iii) to help foster a culture of data sharing, including developing software to make sharing easier. The PSI has had major impact in the past 19 years, where we are now in a situation where most proteomics data sets are readily available, in formats that support critical assessment of results, and allow for data re-purposing.

    The PSI’s activities have largely been divided in two main branches - molecular interactions (MI) and mass spectrometry (MS)-based workflows, with the main highlights being the development of widely used standard formats (https://www.psidev.info), and international cooperation for data submission and access, coordinated through the ProteomeXchange (http://www.proteomexchange.org/) and IMEx (www.imexconsortium.org) Consortia. These developments have been essential in the context of the HUPO Human Proteome Project.

    The current make-up of the PSI involves six working groups - MS, Proteome Informatics, MI, Protein Modifications (MOD), Quality Control (QC) and a recent addition: Intrinsically Disordered Proteins (IDP). We also have a group dedicated to coordination of activity with parallel efforts in metabolomics.

    The roster of current PSI leadership is available at https://www.psidev.info/roles. We would like to bring to the attention of the proteomics community that are planning refresh roles for working group Chairs and co-Chairs in 2021, particularly in the Proteome Informatics area. We are also searching for a new PSI Editor. If you would like to nominate yourself or someone else for a role as Chair, co-Chair or other role within a working group, please email to andrew.jones@liverpool.ac.uk to start the conversation. We would expect that individuals would have had some involvement before in PSI activities, but of course we are a fully open organisation, and always welcome new members.

    In March 2021, we held our annual PSI Spring Workshop (fully online for the second time). The main focal points of the meeting were:

    MI: This track (www.psidev.info/groups/molecular-interactions) has been responsible for the creation and maintenance of several different data exchange formats (PSI-I XML2.5, PSI-MI XML3.0, MITAB2.5-2.8, MI-JSON) and the accompanying controlled vocabulary (PSI-MI CV), and this year focused on a number of new use cases, modeling these to the existing standards to ensure that these were still fit for purpose. Use case examples included contextual interactions, the interactome of a specific cell or tissue type and dynamic interactions, the sequential changes in the composition of these interactome over time or in response to an agonist or inhibitor. We agreed upon a major refactoring of the genetic interaction branch of the PSI-MI CV and discussed methods for linking entities derived from the same gene e.g. proteins and their originating mRNAs, in a network. Finally, we held the annual IMEx Consortium meeting, with participating databases and data users in attendance. We are open to welcoming new members interested in curating molecular interactions or in further developing data standards.

    MS/PI: This track touched on many different topics in an effort to gather input from those participants who do not regularly participate in the ongoing development. We began with a session exploring how the PSI might contribute to the emerging field of non-MS affinity-based workflows, and then moved on to the nearly-ratified Universal Spectrum Identifier (USI) standard. We discussed the ProForma 2.0 in-development standard for proteoform and peptidoform notation, and the PROXI application programming interface for programmatically exchanging proteomics information between ProteomeXchange resources. We explored a proposed extension of the existing mzIdentML and mzTab standards for glycoproteomics, and a proposed format (called SDRF-Proteomics) for the annotation of the relationship between samples and data files in proteomics datasets, aiming to capture the experimental design. We finished the workshop with discussions on the emerging PSI Spectral Library Format (mzSpecLib), an update of mzTab for proteomics, and a binary version of mzML called mzMLb. The MS/PI working group aims to ratify and release several of these formats in the coming year and welcomes additional participation. Several MS/PI members also participated in efforts in the MOD working group, to produce updates to the PSI modification controlled vocabulary that is used across a range of standards in both the MI and MS spaces.

    QC: Across all of biological MS, efforts to increase repeatability and reproducibility of experimentation has become a priority. Communicating quality information in a standardized way has the potential to improve interaction between quality metric-generating software (e.g. reporting the fraction of all MS/MS scans being identified in an LC-MS/MS experiment) and quality decision-making frameworks (e.g. recognizing an LC-MS/MS experiment is an outlier). The mzQC format specification should shortly be released for public comment. It is distinctive for being one of the first HUPO-PSI formats to employ lightweight JSON notation rather than XML, while continuing to define the terms employed in mzQC in a CV.

    IDP: The recently formed Intrinsically Disordered Proteins group (https://www.psidev.info/groups/intrinsically-disordered-proteins), is aimed with understanding and sharing data on disordered regions of proteins, particularly developing annotation standards for structural and structure-function attributes. The group is starting to work on reporting guidelines, and data standards for describing annotations in tab-based and XML formats.

    What all of these efforts have in common is that proteomics (and metabolomics) researchers need ways to communicate their results in a way that is verifiable and trustworthy. Already we have seen a sizable impact from these efforts; analytical chemists that use SCIEX instruments can post to a repository both mzML-formatted data and WIFF files, for example, to ensure that laboratories that do not have access to vendor software can still make use of their MS experiments. Another example is that bioinformatics researchers seeking to optimize the classification of PSMs into accepted and rejected collections can work from the mzIdentML PSMs reported for a wide variety of database search algorithms in thousands of experiments.

    The PSI continues to make rapid progress in its mission to facilitate data sharing and access in the proteomics community, but needs additional participation from the community at all levels to maintain momentum. In addition to the need to support novel approaches and workflows in the field, an additional point of interest is the integration of proteomics with other omics data types and approaches. Will you join us?

  • 30 Apr 2021 1:30 PM | Anonymous member (Administrator)

    Written by Henry Rodriguez, National Cancer Institute, USA

    Born out of the Human Genome Project, the field of genomics evolved with phenomenal speed into a dominant scientific force and opened new avenues to discover cures to diverse diseases… especially in oncology. And as quickly as genomics grew, today we again find ourselves in the midst of a new revolution in science. This new revolution is enabled by the convergence of genomics with proteomics, whose collective goals are to achieve a comprehensive understanding of the information encoded in the genetic material of organisms and how it directs the organization and function of living systems.

    What we are now seeing in proteomics is a science discipline that seems to be at an inflection point, that is the result of widespread technological advances (analytical and computational, standardized workflows ensuring data rigor and reproducibility, and data sharing with the public) and an acknowledgement that genomic data alone do not always provide sufficient insights into the molecular classification of cancer in modern medicine. The outlook for proteomics has brightened substantially. And while today we assess these advances with optimism (and pessimism) as it pertains to precision medicine, the road taken to where proteomic advances are today has not been easily traveled.

    At the U.S. National Cancer Institute, National Institutes of Health, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) was established to address these advances in the field of oncology. Its initial goal was to standardize proteomic methods to ensure rigor and reproducibility of large-scale protein measurements among laboratories, done in coordination with the U.S. Food and Drug Administration and the American Association for Cancer Research. Having achieved this goal, CPTAC then applied its standardized proteomics workflows to three previously genomically characterized tumor types from TCGA (proteogenomics), that revealed additional layers of molecular information not possible through genomics alone. The success of these activities by demonstrating the benefit and need of integrating proteomics with genomics to produce a more unified understanding of cancer, led the NCI to expand CPTAC’s proteogenomics tumor characterization program and for the very first time, to partner with NCI-supported clinical trials.

    The reality is that proteomics and genomics are not competitors. Rather, they are partners. Together, along with other “omics” approaches, they promise to reveal molecular patterns spanning multiple layers of biology and informing new approaches to diagnostics and therapeutics. These complementary approaches stand to make precision medicine a reality.

    The CPTAC program took a risk and in doing so pioneered the emerging field of cancer proteogenomics, while perhaps more importantly restoring interest and enthusiasm in the use of proteomics in the cancer community. To commemorate the advances in science made by the CPTAC program to accelerate our understanding of the molecular basis of cancer through the application of large-scale proteome and genome analysis, and the program’s commitment to creating public resources (data, assays, and reagents [antibodies]) that are utilized by the cancer research community, Cell Press has created an online space dedicated to archiving CPTAC research (https://www.cell.com/consortium/CPTAC) that has and will be published in its family of journals. Also included below are papers that are a collaboration between CPTAC and the International Cancer Proteogenome Consortium (ICPC; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002958). Collectively these papers provide strong resource-based frameworks to better understand a range of human cancers through the lens of precision oncology and will be valuable in informing effective treatment options.

    Furthermore, to understand where colleagues and I see cancer research headed in the next decade, a perspective article was recently published where we examine cancer through the lens of comprehensive molecular characterization of tumors from cancer patients. In this article (https://www.cell.com/cell/fulltext/S0092-8674(21)00285-3) titled “The Next Horizon in Precision Oncology: Proteogenomics to Inform Cancer Diagnosis and Treatment,” we describe the significant contributions of The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) to multidisciplinary collaborative team science and precision oncology, and make the case that proteogenomics needs to be fully integrated into clinical trials and patient care. This approach of genomic and proteomic markers, we believe, will further enable precision oncology to deliver the right cancer treatment to the right patient at the right dose and at the right time.

  • 30 Apr 2021 12:59 PM | Anonymous member (Administrator)

    Written by Emily Hashimoto-Roth, University of Ottawa, Canada

    The month of May will see the start of the Early Career Research Initiative’s (ECR) new interactive panel series! This series, organized in collaboration with the EuPA’s Young Proteomics Investigators Club, will be hosting its inaugural panel discussion on May 17th at 7PM EDT (GMT-4/New York Time), 4PM PDT (GMT-7/Los Angeles Time) and 7 AM CST (GMT+8/Taipei Time) on May 18th. Guests will have the opportunity to hear from and ask questions to our wonderful speakers, Dr. Yu-Ju Chen (Academia Sinica, Taiwan and HUPO President), Dr. Renã A. S. Robinson (Vanderbilt University, USA) and Dr. Robert Rivers (National Institutes of Health, USA), as they discuss the effective promotion of diversity in proteomics. Chairing the inaugural session will be the ECR’s Emily Hashimoto-Roth (University of Ottawa, Canada). To register, please use the following link: https://us06web.zoom.us/meeting/register/tZcsfuugrT8qG9HJGsyNWCzlt9d17pwedSWZ. Register early! There is a limited attendance! Get your questions ready, we cannot wait to see you there!


    Dr. Yu-Ju Chen, Academia Sinica, Taiwan and HUPO President



    Dr. Renã A. S. Robinson, Vanderbilt University, USA

     


    Dr. Robert Rivers, National Institutes of Health, USA




  • 29 Jan 2021 1:41 PM | Anonymous member (Administrator)

    By Michelle Hill, QIMR Berghofer Medical Research Institute, Brisbane, Australia

    It has been a pleasure to serve as HUPOST editor and HUPO Secretary General for the past 2 years. I would like to thank our staff editor Amanda, HPP and ECR news co-ordinators for their continued dedication to HUPOST and the HUPO community. A highlight for 2020 was the “Proteomics in Action” article series that showcased global proteomics uses in everyday life from forensics, clinical diagnostic, drug development to archeology and marine science. Particular thanks go to Stephen Pennington for his enthusiasm and support, as well as all contributors and the people featured.

    I now pass the reins of HUPOST editor to Ben Garcia. Ben is currently the John McCrea Dickson, MD, Presidential Professor in the Department of Biochemistry and Biophysics, and Director of Quantitative Proteomics at the University of Pennsylvania School of Medicine. His research interests include applying mass spectrometry based proteomics for understanding epigenetic mechanisms in human disease, presenting his work at many HUPO World Congress meetings in the past. Ben has been on the Board of Directors of the United States HUPO since 2011, and served on the HUPO Council since 2016. In addition to his recent election to the HUPO Executive Committee as Member-at-Large, Ben has also joined the Marketing & Membership Committee. Hence, he is well-placed to ensure HUPOST fulfils both HUPO member communication needs and marketing strategies.

    All HUPO members can submit proteomics related announcements (workshops, courses, job openings) for consideration for HUPOST, which is sent out monthly to the HUPO mailing list. If you have any ideas for HUPOST, please reach out to Ben via office@hupo.org.

  • 28 Jan 2021 4:44 PM | Anonymous member (Administrator)

    Emily Hashimoto-Roth is a graduate student at the University of Ottawa pursuing a Master’s in Biochemistry specializing in Bioinformatics, under the co-supervision of Dr. Mathieu Lavallée-Adam and Dr. Steffany Bennett. Having obtained an H.B.Sc. in Biopharmaceutical Science at the University of Ottawa, her current research focuses on the design of statistical models and machine learning algorithms to mine and analyze protein-protein interaction datasets. She is a trainee within the NSERC-CREATE Metabolomics Advanced Training and International Exchange Program (MATRIX), further diversifying her graduate studies. In addition to her studies, she is the Director of Communications for a Canadian federal non-for-profit organization called Pulsar Collective, whose mission is to improve gender equality in STEM. She is also a member of the Canadian National Proteomics Network’s Operations Management Team, which works to advance the proteomics field by fostering a community for researchers to meet and collaborate.

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