{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T22:52:27Z","timestamp":1774047147019,"version":"3.50.1"},"reference-count":24,"publisher":"Wiley","issue":"20","license":[{"start":{"date-parts":[[2014,8,21]],"date-time":"2014-08-21T00:00:00Z","timestamp":1408579200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EU FP7","award":["260558"],"award-info":[{"award-number":["260558"]}]},{"name":"Wellcome Trust","award":["WT101477MA"],"award-info":[{"award-number":["WT101477MA"]}]}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2014,10]]},"abstract":"<jats:p>The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission and dissemination of MS\u2010based proteomics data in the public domain. In the consortium, the PRIDE database at the European Bioinformatics Institute, acts as the initial submission point of MS\/MS data sets. In this manuscript, we explain step by step the submission process of MS\/MS data sets to PX via PRIDE. We describe in detail the two available workflows: \u2018complete\u2019 and \u2018partial\u2019 submissions, together with the available tools to streamline the process. Throughout the manuscript, we will use one example data set containing identification and quantification data, which has been deposited in PRIDE\/ProteomeXchange with the accession number PXD000764 (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/proteomecentral.proteomexchange.org\/dataset\/PXD000764\">http:\/\/proteomecentral.proteomexchange.org\/dataset\/PXD000764<\/jats:ext-link>).<\/jats:p>","DOI":"10.1002\/pmic.201400120","type":"journal-article","created":{"date-parts":[[2014,7,21]],"date-time":"2014-07-21T18:09:32Z","timestamp":1405966172000},"page":"2233-2241","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":54,"title":["How to submit MS proteomics data to ProteomeXchange via the PRIDE database"],"prefix":"10.1002","volume":"14","author":[{"given":"Tobias","family":"Ternent","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL\u2010EBI), Wellcome Trust Genome Campus  Hinxton Cambridge UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Attila","family":"Csordas","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL\u2010EBI), Wellcome Trust Genome Campus  Hinxton Cambridge UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Da","family":"Qi","sequence":"additional","affiliation":[{"name":"Institute of Integrative Biology University of Liverpool  Liverpool UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guadalupe","family":"G\u00f3mez\u2010Baena","sequence":"additional","affiliation":[{"name":"Institute of Integrative Biology University of Liverpool  Liverpool UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert J.","family":"Beynon","sequence":"additional","affiliation":[{"name":"Institute of Integrative Biology University of Liverpool  Liverpool UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew R.","family":"Jones","sequence":"additional","affiliation":[{"name":"Institute of Integrative Biology University of Liverpool  Liverpool UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henning","family":"Hermjakob","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL\u2010EBI), Wellcome Trust Genome Campus  Hinxton Cambridge UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3905-4335","authenticated-orcid":false,"given":"Juan Antonio","family":"Vizca\u00edno","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL\u2010EBI), Wellcome Trust Genome Campus  Hinxton Cambridge 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