Newsletter of the Human Proteome Organization

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  • 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!

  • 30 Aug 2019 11:48 AM | Anonymous member (Administrator)

    Early Career Research (ECR) Committee

    The HUPO ECR committee has an open position for a member at the post-doctoral fellow or junior faculty level. This member would be responsible for the communications of the initiative. The member’s tasks would include, but not limited to:

    • Interacting and participating with the ECR committee to grow and support proteomics for early stage investigators.
    • Maintaining and upgrading the HUPO ECR website,
    • Managing the HUPO ECR social media accounts (Twitter, Facebook, Instagram),
    • Assembling material for the HUPO HUPOST monthly emails.
    • Participating in the planning ECR events at International HUPO and other HUPO related events.

    In addition, the member would be expected to participate to the monthly calls with all committee members.

    This position represents a fantastic opportunity for early career researchers to network with other junior scientists and also several senior leaders in the Proteomics field. The member will also have the occasion to develop his own leadership and management skills in an international organization.

    The member should be ready for a commitment of two years to the ECR initiative.

    Interested candidates can contact Mathieu Lavallée-Adam (mathieu.lavallee@uottawa.ca) if they have any questions or to signify their interest before September 8th. It should be noted that the ECR initiative is committed to equity, diversity and inclusion principles and that these, along with geographic diversity will be considered to fill this position.

  • 30 Aug 2019 11:16 AM | Anonymous member (Administrator)

    Early Career Researcher Committee

    The Early Career Researcher (ECR) initiative has prepared numerous exciting activities for the upcoming HUPO World Congress. The following activities will highlight ECR talents and provide junior scientists with unique development opportunities.

    1. All ECRs are invited to register and attend the ECR Mentoring Day on September 15th, where they will interact with senior mentors and learn how to communicate, manage and network more effectively. For more information, please visit: https://www.hupo2019.org/mentoring-day-2/

    2. The three finalists of the Early Career Researcher Manuscript Competition will be giving talks at the World Congress. Come hear about their research during the following sessions:

    • Bioinformatics and Statistics, (Maggie Lam - Sept 17, 10:40AM – 12:40PM),
    • Proteogenomic, (Ankit Sinha - Sept 17, 3:15PM - 5:15PM)
    • The Interactome (Eneko Villanueva - Sept 18, 1:30PM - 3:30PM).

    For more details about the finalists, please visit: https://hupo.org/Early-Career-Researcher-Competition-2019

    3. The eight finalists of the Ph.D. Poster competition will be giving short talks in Adelaide. All are invited to discover their work. The competition finalists are listed here.

  • 30 Jul 2019 4:51 PM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands 

    The Newsletter summarizes all C-HPP related news and activities from May 2018 to July 2019. The Newsletter starts with the Editorial of Christopher Overall, C-HPP Chair, summarizing the current status of the international efforts to find evidence on missing proteins (PE2-4), making c.a. 89% completion and future direction of neXt-CP50. Next, the article entitled “Services for cDNA clones: New Resources for the Dark Proteome Research” by Joshua LaBaer presents the world’s largest collection of unique, full-length Gateway plasmids representing more than 89% (covering 17,362 unique genes) of 19,522 human protein-coding genes made by the chromosome 10 team. These clones and the cloning facility to prepare new clones for sequence variants are available at Arizona State University and can be used to prepare recombinant proteins that can support both confirmation of missing proteins and functional characterization of uPE1 proteins.

    The Newsletter also gives highlights on recent C-HPP Workshops such as the 19th C-HPP workshop in Santiago, Spain, June 16-17, 2018, the 20th HPP Post-Congress Workshop as follow-up of HUPO 2018, in Orlando, USA on October 4, 2018, and the 21st C-HPP Workshop entitled “Illuminating the Dark proteome”, Saint Malo, France, May 11-14, 2019. Besides workshop highlight organizational changes such as introduction of new neXt-CP50 program, election of new (co-)chairs and chromosome PIs. The update of the neXt-MP50 project documented the evidence for new candidates of 104 MPs, which are listed in the Editorial of JPR 2018 issue. Also other highlighted are the summary on JPR 2018 special issue, plans for the 23rd HUPO C-HPP HPP symposium (C-HPP2020) "From chromosome-centric project to the human proteome" which will be taking place in Russia from 22 to 26 May, 2020. This workshop will be happen aboard on a ship traveling from Saint Petersburg to Valaam Island and back.

    Click here to view the C-HPP Newsletter No.8.

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