title: The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.
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.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Attila
authors.initials: A
authors.lastname: Csordas
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Sun
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Jarnuczak
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Riverol
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Tobias
authors.initials: T
authors.lastname: Ternent
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Campbell
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Manuel
authors.initials: M
authors.lastname: Bernal-Llinares
authors.affiliation: Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, Japan.
authors.forename: Shujiro
authors.initials: S
authors.lastname: Okuda
authors.affiliation: Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa 277-0871, Japan.
authors.forename: Shin
authors.initials: S
authors.lastname: Kawano
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Moritz
authors.affiliation: 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.
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Carver
authors.affiliation: 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.
authors.forename: Mingxun
authors.initials: M
authors.lastname: Wang
authors.affiliation: Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Ishihama
authors.affiliation: 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.
authors.forename: Nuno
authors.initials: N
authors.lastname: Bandeira
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.|National Center for Protein Sciences, Beijing, China.
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK juan@ebi.ac.uk.
authors.forename: Juan Antonio
authors.identifier: 0000-0002-3905-4335
authors.initials: JA
authors.lastname: Vizcaíno
mesh_terms: D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry; D020543:Proteome; D040901:Proteomics / Q000379:methods; D057386:Search Engine; D012984:Software; D064878:Web Browser; D057188:Workflow
chemical_list: D020543:Proteome