title: How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
abstract: The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission and dissemination of MS-based 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: 'complete' and 'partial' 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 (http://proteomecentral.proteomexchange.org/dataset/PXD000764).
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Tobias
authors.initials: T
authors.lastname: Ternent
authors.forename: Attila
authors.initials: A
authors.lastname: Csordas
authors.forename: Da
authors.initials: D
authors.lastname: Qi
authors.forename: Guadalupe
authors.initials: G
authors.lastname: Gómez-Baena
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Beynon
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
mesh_terms: D000818:Animals; D030562:Databases, Protein; D006801:Humans; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*; D057188:Workflow
keywords: Bioinformatics; Data standard; Data submission; Data visualization; Proteomics repositories