The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

被引：564

作者：

Deutsch, Eric W. ^{[1
]}

Bandeira, Nuno ^{[2
,3
,4
]}

Sharma, Vagisha ^{[5
]}

Perez-Riverol, Yasset ^{[6
]}

Carver, Jeremy J. ^{[2
,3
,4
]}

Kundu, Deepti J. ^{[6
]}

Garcia-Seisdedos, David ^{[6
]}

Jarnuczak, Andrew F. ^{[6
]}

Hewapathirana, Suresh ^{[6
]}

Pullman, Benjamin S. ^{[2
,3
,4
]}

Wertz, Julie ^{[2
,3
,4
]}

Sun, Zhi ^{[1
]}

Kawano, Shin ^{[7
,8
]}

Okuda, Shujiro ^{[9
]}

Watanabe, Yu ^{[9
]}

Hermjakob, Henning ^{[6
,10
]}

MacLean, Brendan ^{[5
]}

MacCoss, Michael J. ^{[5
]}

Zhu, Yunping ^{[10
]}

Ishihama, Yasushi ^{[11
]}

Vizcaino, Juan A. ^{[6
]}

机构：

[1] Inst Syst Biol, Seattle, WA 98109 USA

[2] Univ Calif San Diego, Ctr Computat Mass Spectrometry, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA

[5] Univ Washington, Seattle, WA 98195 USA

[6] European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England

[7] Toyama Univ Int Studies, Fac Contemporary Soc, Toyama 9301292, Japan

[8] Res Org Informat & Syst, Joint Support Ctr Data Sci Res, Database Ctr Life Sci DBCLS, Chiba 2770871, Japan

[9] Niigata Univ, Grad Sch Med & Dent Sci, Niigata 9518510, Japan

[10] Beijing Inst Life Omics, Natl Ctr Prot Sci Beijing, Beijing Proteome Res Ctr, State Key Lab Prote, Beijing 102206, Peoples R China

[11] Kyoto Univ, Grad Sch Pharmaceut Sci, Kyoto 6068501, Japan

来源：

NUCLEIC ACIDS RESEARCH | 2020年 / 48卷 / D1期

基金：

英国生物技术与生命科学研究理事会; 美国国家科学基金会; 欧盟地平线“2020”; 英国惠康基金;

关键词：

MASS-SPECTROMETRY; PEPTIDEATLAS; STANDARDS;

D O I：

10.1093/nar/gkz984

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteornexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama Public (USA). We first describe the updated submission guidelines, now expanded to include six members. Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies. At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years. In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources. At last, we also outline some of our future plans for the coming years.

引用

页码：D1145 / D1152

页数：8

共 42 条

[1] OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes [J].

Brunet, Marie A. ;

Brunelle, Mylene ;

Lucier, Jean-Francois ;

Delcourt, Vivian ;

Levesque, Maxime ;

Grenier, Frederic ;

Samandi, Sondos ;

Leblanc, Sebastien ;

Aguilar, Jean-David ;

Dufour, Pascal ;

Jacques, Jean-Francois ;

Fournier, Isabelle ;

Ouangraoua, Aida ;

Scott, Michelle S. ;

Boisvert, Francois-Michel ;

Roucou, Xavier .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D403-D410

[2] Open source system for analyzing, validating, and storing protein identification data [J].

Craig, R ;

Cortens, JP ;

Beavis, RC .

JOURNAL OF PROTEOME RESEARCH, 2004, 3 (06) :1234-1242

[3] Ensembl 2019 [J].

Cunningham, Fiona ;

Achuthan, Premanand ;

Akanni, Wasiu ;

Allen, James ;

Amode, M. Ridwan ;

Armean, Irina M. ;

Bennett, Ruth ;

Bhai, Jyothish ;

Billis, Konstantinos ;

Boddu, Sanjay ;

Cummins, Carla ;

Davidson, Claire ;

Dodiya, Kamalkumar Jayantilal ;

Gall, Astrid ;

Giron, Carlos Garcia ;

Gil, Laurent ;

Grego, Tiago ;

Haggerty, Leanne ;

Haskell, Erin ;

Hourlier, Thibaut ;

Izuogu, Osagie G. ;

Janacek, Sophie H. ;

Juettemann, Thomas ;

Kay, Mike ;

Laird, Matthew R. ;

Lavidas, Ilias ;

Liu, Zhicheng ;

Loveland, Jane E. ;

Marugan, Jose C. ;

Maurel, Thomas ;

McMahon, Aoife C. ;

Moore, Benjamin ;

Morales, Joannella ;

Mudge, Jonathan M. ;

Nuhn, Michael ;

Ogeh, Denye ;

Parker, Anne ;

Parton, Andrew ;

Patricio, Mateus ;

Salam, Ahamed Imran Abdul ;

Schmitt, Bianca M. ;

Schuilenburg, Helen ;

Sheppard, Dan ;

Sparrow, Helen ;

Stapleton, Eloise ;

Szuba, Marek ;

Taylor, Kieron ;

Threadgold, Glen ;

Thormann, Anja ;

Vullo, Alessandro .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D745-D751

[4] Locus Reference Genomic sequences: an improved basis for describing human DNA variants [J].

Dalgleish, Raymond ;

Flicek, Paul ;

Cunningham, Fiona ;

Astashyn, Alex ;

Tully, Raymond E. ;

Proctor, Glenn ;

Chen, Yuan ;

McLaren, William M. ;

Larsson, Pontus ;

Vaughan, Brendan W. ;

Beroud, Christophe ;

Dobson, Glen ;

Lehvaeslaiho, Heikki ;

Taschner, Peter E. M. ;

den Dunnen, Johan T. ;

Devereau, Andrew ;

Birney, Ewan ;

Brookes, Anthony J. ;

Maglott, Donna R. .

GENOME MEDICINE, 2010, 2

[5] PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows [J].

Deutsch, Eric W. ;

Lam, Henry ;

Aebersold, Ruedi .

EMBO REPORTS, 2008, 9 (05) :429-434

[6] Proteomics Standards Initiative: Fifteen Years of Progress and Future Work [J].

Deutsch, Eric W. ;

Orchard, Sandra ;

Binz, Pierre-Alain ;

Bittremieux, Wout ;

Eisenacher, Martin ;

Hermjakob, Henning ;

Kawano, Shin ;

Lam, Henry ;

Mayer, Gerhard ;

Menschaert, Gerben ;

Perez-Riverol, Yasset ;

Salek, Reza M. ;

Tabb, David L. ;

Tenzer, Stefan ;

Vizcaino, Juan Antonio ;

Walzer, Mathias ;

Jones, Andrew R. .

JOURNAL OF PROTEOME RESEARCH, 2017, 16 (12) :4288-4298

[7] Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1 [J].

Deutsch, Eric W. ;

Overall, Christopher M. ;

Van Eyk, Jennifer E. ;

Baker, Mark S. ;

Palk, Young-Ki ;

Weintraub, Susan T. ;

Lane, Lydie ;

Martens, Lennart ;

Vandenbrouck, Yves ;

Kusebauch, Ulrike ;

Hancock, William S. ;

Hermjakob, Henning ;

Aebersold, Ruedi ;

Moritz, Robert L. ;

Omenn, Gilbert S. .

JOURNAL OF PROTEOME RESEARCH, 2016, 15 (11) :3961-3970

[8] Development of data representation standards by the human proteome organization proteomics standards initiative [J].

Deutsch, Eric W. ;

Albar, Juan Pablo ;

Binz, Pierre-Alain ;

Eisenacher, Martin ;

Jones, Andrew R. ;

Mayer, Gerhard ;

Omenn, Gilbert S. ;

Orchard, Sandra ;

Vizcaino, Juan Antonio ;

Hermjakob, Henning .

JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION, 2015, 22 (03) :495-506

[9] PASSEL: The PeptideAtlas SRM experiment library [J].

Farrah, Terry ;

Deutsch, Eric W. ;

Kreisberg, Richard ;

Sun, Zhi ;

Campbell, David S. ;

Mendoza, Luis ;

Kusebauch, Ulrike ;

Brusniak, Mi-Youn ;

Huettenhain, Ruth ;

Schiess, Ralph ;

Selevsek, Nathalie ;

Aebersold, Ruedi ;

Moritz, Robert L. .

PROTEOMICS, 2012, 12 (08) :1170-1175

[10] Updated MS2PIP web server delivers fast and accurate MS2 peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques [J].

Gabriels, Ralf ;

Martens, Lennart ;

Degroeve, Sven .

NUCLEIC ACIDS RESEARCH, 2019, 47 (W1) :W295-W299

← 1 2 3 4 5 →