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

Big Data Computational Biology / methods Data Mining Databases, Protein Proteomics / methods Software Software Design Web Browser

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
08 01 2020
Historique:
accepted: 14 10 2019
revised: 11 10 2019
received: 14 09 2019
pubmed: 7 11 2019
medline: 19 5 2020
entrez: 6 11 2019
Statut: ppublish

Résumé

The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.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.

Identifiants

DOI: 10.1093/nar/gkz984 PMID: 31686107 PMC: PMC7145525
pubmed: 31686107
pii: 5612546
doi: 10.1093/nar/gkz984
pmc: PMC7145525
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

D1145-D1152

Subventions

Organisme : NIGMS NIH HHS
ID : P41 GM103533
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM087221
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM103551
Pays : United States
Organisme : NIGMS NIH HHS
ID : R24 GM127667
Pays : United States

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Eric W Deutsch (EW)

Institute for Systems Biology, Seattle, WA 98109, USA.

Nuno Bandeira (N)

Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.

Vagisha Sharma (V)

University of Washington, Seattle, WA 98195, USA.

Yasset Perez-Riverol (Y)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Jeremy J Carver (JJ)

Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.

Deepti J Kundu (DJ)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

David García-Seisdedos (D)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Andrew F Jarnuczak (AF)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Suresh Hewapathirana (S)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Benjamin S Pullman (BS)

Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.

Julie Wertz (J)

Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.

Zhi Sun (Z)

Institute for Systems Biology, Seattle, WA 98109, USA.

Shin Kawano (S)

Faculty of Contemporary Society, Toyama University of International Studies, Toyama 930-1292, Japan.
Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba 277-0871, Japan.

Shujiro Okuda (S)

Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.

Yu Watanabe (Y)

Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.

Henning Hermjakob (H)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China.

Brendan MacLean (B)

University of Washington, Seattle, WA 98195, USA.

Michael J MacCoss (MJ)

University of Washington, Seattle, WA 98195, USA.

Yunping Zhu (Y)

State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China.

Yasushi Ishihama (Y)

Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.

Juan A Vizcaíno (JA)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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