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Newsletter of the Human Proteome Organization

Current and past HUPOSTs are posted here for your review. Stories, highlights, news, and announcements are gladly accepted for inclusion in the HUPOST. Please submit your information to the HUPO Office at office@hupo.org.

FEATURED ARTICLES


  • 29 Nov 2019 10:43 AM | Anonymous member (Administrator)

     

    Chris Overall, University of British Columbia, Canada

    Publishing in the first week of December, the seventh annual special issue of the Journal of Proteome Research dedicated to the HPP has 20 major contributions from the two HPP initiatives, the Chromosome-centric HPP (C-HPP) and the Biology/Disease (B/D-HPP) HPP, and four Resource Pillars in Mass Spectrometry, Antibody-Profiling, Knowledgebase, and Pathology.

    Based on the January 2019 updates of curation and annotation of the human proteome by neXtProt (https://www.nextprot.org/) from the standardized reanalysis of mass spectrometry datasets by PeptideAtlas (http://www.peptideatlas.org/), which form the baseline for the 2019 papers in this special issue, Omenn et al (2019) report that highly credible evidence supports Protein Evidence Level 1 (PE1) for 17,694 protein-coding genes, 89.3% of the total of 19,823 predicted human protein-coding genes. In this annual metrics of the human proteome paper, these numbers represent a net increase of 224 PE1 proteins, due to promotion of 213 PE2,3,4 entries to PE1, but with a net decrease of only 57 missing proteins (MPs) due to 60 PE1 demotions and 116 new PE2,3,4 entries.

    Many strategies have been deployed to detect the neXtProt missing proteins: analysis of more diverse specimens including the first large scale proteome analysis of young adult human bone, use of much more sensitive mass spectrometry instruments, enrichment of low-abundance proteins, solubilization of membrane proteins, and the use of multiple proteases. This year’s Special Issue continues that endeavor.

    Shteynberg et al 2019 have developed PTMProphet, open-source software for facilitating the calculation of confidence metrics for the precise localization of PTMs. Since its associated algorithms were integrated into the Trans-Proteomic Pipeline platform, this tool has been used to assess PTMs with different numbers of modifications and modified sites using the information content to yield correct localization for 1164 PTMs at less than a 1% false localization rate.

    These are but a few highlights of the important compilation of papers highlighting the progress of the HPP.

    Omenn, G. S.; Lane, L.; Overall, C. M.; Corrales, F. J.; Schwenk, J. M. et al., Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project. J Proteome Res 2019.

    Deutsch, E. W.; Lane, L.; Overall, C. M.; Bandeira, N.; Baker, M. S. et al. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. J Proteome Res 2019.

    Shteynberg, D. D.; Deutsch, E. W.; Campbell, D. S.; Hoopmann, M. R.; Kusebauch, U. et al., PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. J Proteome Res 2019.

    The new HPP Data Guidelines v 3.0
    A key paper that needs close attention in the hunt for missing proteins is from Deutsch and colleagues 2019 who now report the HPP Guidelines v3.0, based on wide consultations with the HPP community over the past year. Key features of v3.0 are a reorganized main checklist, addition of guidelines for data-independent acquisition workflows and for use of the Universal Spectrum Identifier developed by the HUPO Proteomics Standards Initiative (PSI), an updated HPP pipeline for standardized reanalysis of MS datasets generated throughout the community, and a plan for incorporating MassIVE-KB into the HPP pipeline. This timely update maintains the high quality of MS-based data, which is essential for creating a credible chromosome-centric protein parts list for the entire human proteome.

    The C-HPP Wiki
    The C-HPP wiki is continually being updated and we require your input for the individual chromosome teams. Each chromosome group can upload themselves or send their neXt-MP50, neXt-CP50 progress and other updates for their chromosome to Peter Horvatovich (see C-HPP Wiki).

    Chris Overall (chair), Young-Ki Paik (co-chair), Lydie Lane (co-chair), Gilberto B. Domont (MAL), Fernando Corrales (MAL), Pengyuan Yang (MAL) and Peter Horvatovich (secretary general).

  • 29 Nov 2019 9:43 AM | Anonymous member (Administrator)

    Tadashi Yamamoto, Former chair and current co-chair Niigata University, JAPAN.
    John M Arthur, Current chair, University of Arkansas for Medical Sciences ,USA.

    The first-generation HKUPP was established as the 11th initiative in the World HUPO Congress by gathering about 40 researchers from around the world in 2007 with the following missions:

    • To facilitate proteome analysis and foster proteomics researchers in nephrology.
    • To understand kidney functions and pathophysiology of human kidney diseases
    • To provide kidney and urine proteome databases for discovery of biomarkers and drug targets.

    In the next 10 years (2007-2017), the HKUPP members had several meetings during the World HUPO Congresses and the American Society of Nephrology meetings to exchange the data and information on proteomic analysis of kidney tissue and urine samples. As a contribution to urine proteomics researchers, we proposed a guide or recommendation of how to collect and store urine samples suitable for proteome analysis (Sci Transl Med. 2010 Aug 25;2(46):46ps42. doi: 10.1126/scitranslmed.3001249.). Proteome data of urine samples and kidney tissues from normal healthy volunteers were also collected and made available in the HKUPP website (www.hkupp.org). Comparison of the proteomes of these tissues and plasma/urine provided tissue(-compartment)-unique proteins, as well as urinary proteins uniquely derived from these tissues. Those proteins were therefore expected to be proteins that might play specific roles in these tissues, or proteins which might indicate pathological events.

    In 2017 the new chair of HKUPP, Prof. John M Arthur started to re-organize the HKUPP team to promote the second-generation project to apply the current advanced techniques and instruments to clinical samples. Samples such as kidney biopsy specimens and patient urine will be useful to understand pathology and to establish urine biomarkers for clinical assessment (Fig.1).

    In 2019 we had a meeting in Washington DC during the American Society of Nephrology Kidney Week 2019 to discuss the plans related to the 2nd generation HKUPP and the possibility for collaborative grant application such as RC2 of NIH to facilitate the international activities of the HKUPP initiative.

    Figure. 1 Promotion of HKUPP activities from the 1st generation to the 2nd generation: From basic science to clinical contributions


  • 28 Nov 2019 3:31 PM | Anonymous member (Administrator)


    Human 10th birthdays mark a very special tradition – from a learning-packed early childhood to wonderfully exhilarating teenage years. Similarly, at the 19th Human Proteome Organization World Congress in Stockholm, the Human Proteome Project (HPP) celebrates this milestone decadal birthday by releasing the first community-endorsed blueprint draft of the human proteome.

    It was only two decades ago that a company (Celera Genomics) and public rivalry under the Human Genome Project assembled the draft human genome. This contained far fewer protein-coding genes than was anticipated and was jam-packed with gaps and ambiguities. Recent analysis suggests that the human genome only codes for approximately 20,000 proteins. Arms with the draft genome, the first challenge was to assemble a parts-list blueprint for the human proteome. This initial phase involved an unparalleled collaborative enterprise, this time involving scientists from over 100 countries with various skill sets, freely uploading and then communally analyzing their data. This now culminates in a high-precision human proteome knowledge base.

    Some sought to find the elusive missing proteins which dodge discovery, whilst others sought to appreciate how human proteome worked or how it could be harnessed to better diagnose and treat cancer, Alzheimer’s, heart attacks, diabetes, and other diseases.

    Join us in Stockholm, Sweden from October 18 – 22, 2020 to celebrate the launch of the collaborative Human Proteome Project blueprint. Read more.

  • 01 Nov 2019 8:53 AM | Anonymous member (Administrator)

    Chris Overall, University of British Columbia, Canada

    The 23rd C-HPP workshop will be held aboard the very comfortable river-class cruise ship traveling from Saint Petersburg to Valaam Island and back to Saint Petersburg from Friday May 15 (18:00) to Monday May 18 (09:00), 2020. The focus on of the workshop will be “From chromosome-centric project to the human proteome” and will also nucleate celebrations of the 10th anniversary of the C-HPP Initiative. The workshop is organized by Prof. Alexander Archakov, also celebrating in 2020 his 80th birthday and the and 75th Anniversary of the Institute of Biomedical Chemistry (Moscow, Russia). Thus, many Russian Colleagues in Proteomics and Bioinformatics will also be in attendance making for a rich program.

    The Workshop aims to cover the following scientific topics:

    • Status update from Chromosome, neXt-MP50 and neXt-CP50 teams
    • Bioinformatics Tools Development—from C-HPP to the human proteome
    • Transcriptoproteomics—the way from Genome to Proteome
    • Proteomics Technology Innovations
    • Proteomics and other OMICs—Impact on Medicine
    • Missing proteins in rare tissues and diseases (with B/D-HPP)

    Registration will open soon and we are expecting that support from the Russian Government will be announced late in December, at which time we can release the cost. All information regarding the workshop will be available at the C-HPP Wiki.

    The HUPO C-HPP Chronicle
    The Chronicle of the Chromosome-Centric Human Proteome (C-HPP) project showing the most important milestones of the C-HPP such as building up of the chromosome teams, the C-HPP and then the HPP special issues in Journal of Proteome Research, C-HPP workshops and special events, and key publications is available at C-HPP Wiki.

  • 31 Oct 2019 4:29 PM | Anonymous member (Administrator)

    Early Career Research (ECR) Committee

    The HUPO Early Career Researcher (ECR) Initiative is proud to announce that Dr. Justyna Fert-Bober has been nominated as the ECR representative on the HUPO Executive Committee. Dr. Fert-Bober is a co-founder of the HUPO ECR Initiative, a trailblazer and leader in ECR involvement in the proteomics community and a strong advocate of highlighting early career researcher talents. Among other things, she is a co-organizer of the HUPO ECR Manuscript Competition and of the HUPO World Congress Trainee Workshop (Biosketch below).

    This new ECR position on the HUPO Executive Committee was approved by the HUPO Council and announced at the most recent HUPO General Assembly. The HUPO ECR Initiative would like to thank the HUPO Council for their continuous support of proteomics early career researchers and for giving them a voice on the HUPO Executive Committee.


    Dr. Justyna Fert-Bober. Research Scientist I
    Cedars-Sinai Heart Institute 

    Dr. Justyna Fert-Bober’s Biosketch

    Dr. Fert-Bober is a Research Scientist I at the Cedars-Sinai Heart Institute. She obtained her B.Sc. and M.Sc. degrees in Biochemistry and Molecular Biology from the University of Wroclaw and her Ph.D. in Clinical Chemistry from Medical University, Wroclaw. She then performed her postdoctoral research at The Johns Hopkins University School of Medicine. Dr. Fert-Bober is a pioneer in the understanding of arginine deiminases and protein citrullination’s contribution to molecular and cellular mechanisms of heart failure in the general population and in the immunopathogenesis of heart disease in rheumatoid arthritis patients. She has published over 17 papers on these topics. Dr. Fert-Bober’s overarching research goal is to identify panels of biomarkers and drug targets that can be used in the development of novel diagnostic and therapeutic approaches to not only treat patients for a limited time, but to change underline disease processes. In addition, Dr. Fert-Bober is dedicated to raising the profiles of early career researchers. She is the co-founder of the HUPO Early Career Researcher Initiative, which main objectives are to provide training opportunities to early career researchers and to showcase their work and talent on the international stage.

  • 31 Oct 2019 4:26 PM | Anonymous member (Administrator)

    Vera Ignjatovic,University of Melbourne, Australia

    Blood plasma is a highly accessible sample for monitoring the health status of a donor and is, as such, one of the most frequently analyzed specimens for clinical testing. Plasma is therefore a sample type that is also very frequently used in translational research. However, it is a challenging sample for proteomics analysis because a small number of proteins are extremely abundant, making it difficult to assay the very many lower abundance proteins.

    The Human Plasma Proteome Project (HPPP) was launched in 2002 as one of the first initiatives of HUPO with the main aim of uncovering the complexities and defining the protein contents of this key reporter system.

    Today, the HPPP initiative is led by Jochen Schwenk, Eric Deutsch and Vera Ignjatovic a group of proteomics researchers with diverse focus areas. Similar to the body fluid it studies, HPPP is a connecting platform that has collaboration at its core. This became evident in a recent article produced by a multinational and multidisciplinary team of early career researchers, representatives from the industry and senior members of the community.

    The HPPP also aims to support early carrier researchers (ECR) such as Philipp Geyer, who has implemented the rectangular strategy and is working on biomarker discovery in Matthias Mann´s laboratories in Munich and Copenhagen. Philipp joined the HPPP for a plasma proteomics review published in the Journal of Proteome Research last month, allowing him to work in an interactive team of highly experienced proteomics researchers.

    [Ignjatovic V, Geyer PE, Palaniappan KK, Chaaban JE, Omenn GS, Baker MS, Deutsch EW, Schwenk JM. Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data. Journal of Proteome Research]

    HPPP wants to support the community and reflect on the recent improvements in the depth, coverage and speed of studying plasma proteins - either via MS-based approaches or affinity assays. A revived interest in this clinically valuable proteome is accompanied with an increase in the number of MS data sets available to the public, as well as increasing availability of large-scale affinity proteomics data. In addition, links to other omics data types will help to uncover the currently less well understood processes in health, disease, and ageing. The growing resources to build targeted MS as well as affinity-enhanced assays will further expand our understanding of the plasma proteome.

    The HPPP seeking researchers engaged in plasma proteomics projects or anyone interested in advancing the state-of-the-art in plasma proteomics in the future to join the HPPP team. Please contact any of the above co-authors and state your interest in joining this project.

  • 08 Oct 2019 11:37 AM | Anonymous member (Administrator)

    Early Career Research (ECR) Committee

    ECR competition winners
    The ECR initiative would like to congratulate Eneko Villanueva (University of Cambridge) who won the ECR Manuscript Competition with his talk on the “Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)” and Tim Van Den Bossche (Ghent University) who won the Ph.D. Poster Competition with his presentation entitled “ReScoring peptide-to-spectrum-matches based on predicted fragment ion intensities leads to an increased identification rate in metaproteomics”. The ECR initiative also congratulates all finalists of both competitions, who were invited by the Royal Society of Chemistry to a networking dinner, where they had the opportunity to learn about the publication peer review process. Finally, thank you to all senior scientists who participated in the review process for these competitions.


    Fourth from the left Maggie Lam (Runner-up), Enek Villanueva (Winner), and Ankit Sinha (Runner-up).

    HUPO 2019 PH.D. Poster Competition Recipients 


    Fourth from the left Tim Van Den Bossche (Winner), Sayantani Chatterjee (Runner-up) and Maik Mueller (Runner-up).

    Annual Mentoring Day and networking event
    In addition to displaying their proteomics research on the international stage, ECRs had the opportunity to participate in the annual HUPO Mentoring Day, where they gathered advice on how to communicate, manage and network effectively from international proteomics leaders. The ECR initiative thanks Drs. Jennifer Van Eyk, John R. Yates III, Birgit Schilling, Daniel Figeys, Merry Lindsey, and Stuart Cordwell for sharing their experience with the future leaders of the field. Furthermore, over 30 ECRs also had the occasion to mingle at a meet and greet breakfast session generously sponsored by Atturos.

    Thank you for supporting ECRs
    Finally, the ECR initiative would like to thank Prof. Peter Hoffmann and Prof. Stuart Cordwell, the entire organizing committee of the HUPO 2019 World Congress in Adelaide and HUPO for deploying herculean efforts to offer travel funding for ECRs to attend HUPO 2019. Through their work and by reaching out to local communities, they were able to provide travel funding to over 150 ECRs. The ECR initiative would also like to thank the following societies (in no particular order) who partnered to provide travel funding to ECRs: the German Society for Proteome Research (DGPF), the Japanese Proteomics Society (JPrOS), the Korean Human Proteome Organization (KHUPO), the Proteomics Society of India (PSI), the Singapore Society for Mass Spectrometry, the Swiss Proteomics Society, the United States Human Proteome Organization (US-HUPO), and the Australasian Proteomics Society (APS).

  • 08 Oct 2019 10:58 AM | Anonymous member (Administrator)

    Chris Overall (Chair), Young-Ki Paik (Co-Chair), Lydie Lane (co-chair), Gilberto B. Domont (MAL), Fernando Corrales (MAL), Pengyuan Yang (MAL) and Péter Horvatovich (Secretary General).

    The Annual HUPO Congress in 2019 in Adelaide, Australia had a rich C-HPP and HPP program and activities on the future directions of the (C-)HPP programs.

    The HPP investigators day, September 16, 2019

    The HPP investigators Program was held on Sunday, September 15, 2019. The program included a long introduction to “The Human Proteome Project” by Mark Baker, followed by updates and reports on C-HPP and JPR HPP special issue by the C-HPP Chair, Chris Overall, the B/D-HPP by Fernando Corrales, Knowledgebase Pillar by Eric Deutsch, Mass Spectrometry Pillar by Sue Weintraub, Antibody/Affinity Pillar by Jochen Schwenk and the fourth new Pathology Pillar by Dan Chen.

    The program was followed by C-HPP and B/D-HPP Principal Investigator Council meetings in parallel sessions and then by the HPP Workshop on “Illuminating the dark proteome to understand human biology and disease”, where Eric Deutsch presented the HPP Data interpretation Guidelines version 3.0 and Lydie Lane provided an update on new neXtprot developments, such as the support of the PSI Extended Fasta Format (PEFF), which includes annotation of the protein sequences with PTMs and sequence variants using controlled vocabulary, changes on protein evidence levels, definition of protein function serving the basis of uPE1 definition and changes of the number of proteins with known and unknown functions in the current neXtprot release (Jan-2019) compared to the previous release in Jan-2018, integration of variant frequencies from gnomAD database and the future integration of I-TASSER/COFACTOR protein function predictor tools.

    Paola Roncada provided a summary on the Food and Nutrition Proteomics highlighting importance of proteomics in allergen identification such as partially digested shrimp tropomyosin. The Human Kidney and Urine proteome initiative progress was presented by John Arthur, while Meggie Lam presented the PubMed literature analysis of the HPP completed with visualization using VOSviewer.

    HPP Workshop Day, September 19, 2019

    HPP Workshop day started with an intensive and animated discussion on the highlights of HUPO 2019 and current progress and future directions of the HPP by Jennifer van Eyk. Then the future directions of the HPP was highlighted by C-HPP EC by Chris Overall and Young-Ki Paik, B/D-HPP (Ileana Christea), the Pathology Pillar (Dan Chan), and Ab/Affinity Pillar, by the new Chair, Cecilia Lindskog. Discussion led to the presentation of current and future HPP Pillars plans and how to increase in general the visibility of proteomics in the scientific community.

    Th eSPecial Invited C-HPP speaker, Seán O’Donoghue, presented an illuminating lecture on the “The dark proteome of structural biology”, where “dark” represent regions in proteins where there is no known or predicted structure based on every sequence with a structure in the PDB from all species, a brilliant tour de force in bioinformatics and data visualizations using the AQUARIA tool. Missing protein searches in rare tissues such as human bone was summarized by Chris Overall leading to uncomfortable conclusions concerning the likelihood of finding MPs in such tissues, while Fernando Corrales summarized popular and less popular proteins in disease.

    Mike Snyder presented a multi-omics strategy of human health over several years of active monitoring and Lydie Lane the use of SPARQL to query multiple complex databases among others neXtProt allowing to gain more comprehensive information on life-science curated data as strategy for better HPP outreach.

    C-HPP Poster Session

    Three winners of the C-HPP Poster Awards each received a certificate and cheque of USD200 from John Wilson, Protifi at the closing ceremony. The awardees are, Chae-Yeon Kim (Yonsei University, Seoul, Korea), Chengxin Zhang (University of Michigan, Ann Arbor, MI, USA) and Yuanling Zhang, (Siqi Liu Lab, Beijing Institute of Genomics, China).

    Bioinformatics Hub

    Again, Eric Deutsch has mastered a wide ranging and practical program on bioinformatics challenges in MP hunting, data analysis and implementing the new Human Proteome Project Data Interpretation Guidelines (Version 3.0) in a friendly atmosphere that encourages Q & A and for attendees to come away truly knowing the answer to their questions. The program with some of presentations is available at http://bit.ly/hupohub2019.

    The C-HPP Wiki

    The C-HPP wiki was updated with slides of many presentations and a dedicated session of the Bioinformatics hub was provided on how to edit C-HPP Wiki, which is based on Tiki Wiki content management system (version 18.1). We ask input from the individual chromosome teams to fill the C-HPP Wiki with further content regarding resources, achievements, available ProteomeXchange datasets and any information, which is relevant for C-HPP participants and in general for the HPP community.

  • 08 Oct 2019 10:50 AM | Anonymous member (Administrator)

    Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

    Submit your original research, communications or review manuscripts that combine proteomics with other omics techniques to this special issue by 31 May 2020. Find out more here: https://www.mdpi.com/journal/biomolecules/special_issues/multiomics_biomedical_research



  • 08 Oct 2019 9:53 AM | Anonymous member (Administrator)

    Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

    The laid-back city of Adelaide provided a relaxing backdrop for an intensive week of HUPO2019 - a big thank you and congratulations to the local organizing committee!

    In addition to cutting edge science, HUPO Executives, HUPO Council and Presidents of National Proteomics Societies had extensive discussions on future strategies for HUPO. Several areas of development were identified, including:

    • Foster active HUPO community on social media.
    • Add value to HUPO membership and attract new members.
    • Inform the broader public on the importance of proteins.

    It is envisaged that small groups of volunteers will drive specific tasks towards the identified goals, generally within short time frames. We would like to invite members with practical ideas and time to volunteer through this online form. Feedback on current barriers and potential drivers to increase the engagement can also be provided through the same.

    Early Career Researchers (PhD students and postdocs) are particularly encouraged to help build our HUPO community!




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