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Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936. Epub 2016 Oct 18.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Author information

1
Institute for Systems Biology, Seattle, WA 98109, USA.
2
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
3
Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
4
Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan.
5
Center for Computational Mass Spectrometry, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
6
Department Computer Science and Engineering, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
7
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
8
Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.
9
National Center for Protein Sciences, Beijing, China.
10
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK juan@ebi.ac.uk.

Abstract

The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide. We give an overview of the current consortium activities and describe the advances of the past few years. Augmenting the PX founding members (PRIDE and PeptideAtlas, including the PASSEL resource), two new members have joined the consortium: MassIVE and jPOST. ProteomeCentral remains as the common data access portal, providing the ability to search for data sets in all participating PX resources, now with enhanced data visualization components.We describe the updated submission guidelines, now expanded to include four members instead of two. As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions resulting in public data release becoming the norm. More than 4500 data sets have been submitted to the various PX resources since 2012. Human is the most represented species with approximately half of the data sets, followed by some of the main model organisms and a growing list of more than 900 diverse species. Data reprocessing activities are becoming more prominent, with both MassIVE and PeptideAtlas releasing the results of reprocessed data sets. Finally, we outline the upcoming advances for ProteomeXchange.

PMID:
27924013
PMCID:
PMC5210636
DOI:
10.1093/nar/gkw936
[Indexed for MEDLINE]
Free PMC Article

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