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The Biology and Disease Human Proteome Project (B/D-HPP) Annual Report 2017-2018

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The Biology and Disease Human Proteome Project (B/D-HPP) Annual Report 2017-2018 The Biology and Disease Human Proteome Project (B/D-HPP) Annual report 2017-2018 Submitted by Fernando Corrales and Ileana Cristea on behalf of all members and liaisons of the B/D-HPP Executive committee 1 The Biology and Disease Human Proteome Project (B/D-HPP) Annual report 2017-2018 1. Overview and expansion The Biology and Disease-driven Human Proteome Project (B/D-HPP) is focused to support the use of state-of- the-art proteomic methods to characterize and quantify proteins for in-depth understanding of the molecular mechanisms of biological processes and human disease across life sciences. The B/D-HPP is truly a grass root initiative where groups of individual come together globally to address key issues. One goal of the B/D-HPP is to broaden the impact of proteomics to the broader community based on organ and disease areas. A second goal is to develop popular proteins within the B/D-HPP in order to prioritize protein targets that are highly relevant to each particular field to deliver relevant assays for the measurement of these selected targets and to disseminate and make publicly accessible the information and tools generated. At the last International HUPO in Dublin, there were 19 B/D-HPP initiatives with 3 closely related HPP resource pillars. It is from these initiatives that the chairs and the B/D-HPP create 6 main sessions for the international HUPO meeting 2017. These and other groups also have a chance to present and catch up with each other on Sunday and Thursday workshops hosted HPP. An additional effort of the B/D-HPP is to encourage and support the scientific career development of the early career researchers among the HUPO community. In this sense the initiative is strongly contributing to the activities of the early career researchers helping them to create opportunities to present their work at international HUPO congresses (e.g. the ECR manuscript competition) or to interact with more senior HUPO scientists (e.g. the ECR mentoring day). The organization is Fernando Corrales, chair and Ileana Cristea (co-chair) with the most amazing executive committee consisting of Jennifer Van Eyk (past-chair), Gil Omenn (Ex officio), Hui Zhang, Eric Deutsch, Pengyuan Yang, Tadashi Yamamoto, Sanjeeva Srivastava, Paola Roncada and Michelle Hill, Ferdinando Cerciello (ECR representative) and Mark Baker (HPP Chair). 1.a. B/D HPP initiatives activity this year. According to the procedure established last year, we sent out a questionnaire to determine the viability and work being carried out by the various initiatives. The aims were: 1. To update the information about the initiatives on the B/D-HPP initiative page of the HUPO website. We would like to have an updated and attractive picture of the B/D group aims, activity and achievements to facilitate cross interactions with other HPP groups and to attract additional partners from the scientific community. 2. To compile the collected information in a B/D-HPP annual report. That will provide a global view of the B/D-HPP as a whole and will highlight our strengths. 3. To explore the willingness to participate in the HUPO Congress. This is the main HUPO activity and the participation of the B/D groups is highly encouraged by submitting abstracts to the HPP session topics, active inputs in the Sunday and Thursday programs on popular/priority proteins, PTMs, etc. 5. To explore the willingness to prepare manuscripts for the JPR Special Issue. To find new ways of interaction across B/D and C-HPP groups. Results from the questionnaire 2018 Questionnaire B/D HPP An international collaborative project that deals with mapping, annotating and characterizing the proteome using proteomics technologies in its relation to human biology and/or diseases. B/D-HPP provides a framework for the coordination of 19 initiatives that integrate about 50 multi-national research groups. 2 B/D HPP Questionnaire items 1-4 B/D HPP Questionnaire item 6 1. Please state the name of your initiative, name and email of chair and co-chairs, starting date of your B/D initiative and any additional information: 6. Are you currently doing research on popular/priority proteins? 2. What are your main aims? 2.a. Brief statement: Yes: 2.b. Some of the current lines of work include (fill in for your initiative): 80 If not, would you be willing to? 10 2.c. Main achievements in 2017: 70 3. Any related documents you’d like to link? 9 3.a Websites and links (fill in for your initiative): 60 Yes No In the future 8 HBPP Cancer FAN 3.b Papers (fill in for your initiative) 7 3.b.1 Papers published in collaboration within the initiative 50 * CVD HIPP * 6 3.b.2 List Top 5 papers for 2017 40 * HKUPP * 3.c Congresses in 2017? (Committees, lectures… )(fill in for your initiative) * EyeOme 5 30 * 3.c.1 Participation in proteomics meetings in 2017? Liver 4 3.c.2 Participation in congresses organized by other biomedical or clinical associations 20 Mitochondria 3 3.d Other documents 4. Educational and dissemination activity (Courses, workshops, summer schools, etc) in 2017 10 PediOme 2 Plasma 1 0 s s s RAD r e e 0 i e s t s i p r Yes No In the future v a r i t p g c n d a o • e Updated information for each initiative: leadership, participatin c n h • Protein lists available from peptide atlas (https://db.systemsbiology.net/sbeams/cgi/ l o s i i a l t n a laboratories, main aims, plans and activity. Valuable information to b o u n i i PeptideAtlas/proteinList?protein_list_id=45 ). t P a m n keep updated the B/D HPP web page. e r s e • s Five papers already published (EyeOme, Liver and RAD). i t d n I • In addition to the 72 papers (top 5 published by initiatives’ labs) / l a • Two published tools for selecting popular proteins from the literature n o reported by the 13 initiatives answering the questionnaire, 17 were i t a Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. c collaborative efforts of the participating laboratories. u d Lam MP, Venkatraman V1, Xing Y, Lau E, Cao Q2, Ng DC, Su AI3, Ge J2, Van Eyk JE1, Ping P. • Participation in 44 international congressess, 20 on proteomics and E J Proteome Res. 2016 Nov 4;15(11):4126-4134. Epub 2016 Jul 19. 24on other biomedical, clinical disciplines. *Collaborative publications Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining. • Organisation of 30 educational and dissemination related activities. **Proteomics Yu KH, Lee TM, Wang CS, Chen YJ, Ré C, Kou SC, Chiang JH, Kohane IS, Snyder M. ***Biomediacal/clinical J Proteome Res. 2018 Apr 6;17(4):1383-1396. doi: 10.1021/acs.jproteome.7b00772. Epub 2018 Mar 15. B/D HPP Questionnaire item 7 B/D HPP Questionnaire item 8 8. During the analysis of your specific and perhaps unique samples that might be of great value to identify missing proteins. 7. Activities and meetings planned for 2018 • Would you be willing to share raw MS data sets for reanalysis in collaboration with other HPP initiatives? Meeting participation/organization • Would you be willing to share samples? Like what? Initiative HUPO/HPP Others 11 Cancer 1 10 • Would you be willing to run samples from other teams? CVD 1 9 EyeOme 8 Initiative Data Samples Run samples 14 FAN 5 7 Cancer 1 1 1 HBPP 1 3 CVD 1 1 1 12 6 HIPP 1 EyeOme 1 0 0 5 Liver 2 FAN 1 1 1 10 4 HBPP 1 0 0 Mitochondria 1 1 8 3 HIPP IMOP Liver 1 0 1 2 PediOme 1 Mitochondria 1 0 1 6 Plasma 1 1 1 IMOP 1 0 1 4 RAD 1 1 0 PediOme 1 1 1 HUPO/HPP Others Plasma 1 0 1 2 RAD 1 1 1 KUHPP 1 0 1 0 12 5 10 • Some initiatives (HBPP, CVD, Liver, RAD) report activities including setting up Data Samples Run samples analytical methods (for popular proteins in some cases) and preparation of • Data sharing if published or under collaboration publications (new data and reviews). • Type of sample not indicated but in the case of RAD (serum). Difficulties due to • All initiatives attending the HUPO meeting in Orlando were planning to present their regulatory issues work but this has not being included in the agenda. • Availability to run limited number of samples according to capacity. B/D HPP Questionnaire item 10 10. Would your initiative be willing to prepare a data-driven manuscript based around your initiative for the HPP special issue in Journal of Proteome Research? Manuscripts are due by 31 May 2018 Initiative HPP 6 session track Sunday HPP Pis Thursday HPP Early morning Cancer 1 1* 1 1* CVD 1 1 1 1 EyeOme 1 1 1 1 FAN 1 1 1 1 HBPP 1 1 1 1 HIPP 1 0 1 0 Liver 1 1 1 1 Mitochondria 0 0 0 0 IMOP 0 0 0 0 PediOme 1 1 1 1 Plasma 1 1 1 1 RAD 1 1 0 1 KUHPP 1 1 1 1 11 9 10 9 2. Contributions to HUPO Orlando 2018. This year the initiative is involved at International HUPO Sunday: HPP Investigators Meeting Sunday-Wednesday Bioinformatics Hub Monday – Wednesday: B/D-HPP Scientific Track comprising 6 sessions ECR manuscript competition Clinical Fellow Travel Award Thursday: HPP Strategic Workshop 3. Outreach by B/D-HPP to the proteomics and broader scientific community 3.a.
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