title: The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.
abstract: The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
authors.affiliation: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. pst@ebi.ac.uk
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Vizcaíno
authors.forename: Richard G
authors.initials: RG
authors.lastname: Côté
authors.forename: Attila
authors.initials: A
authors.lastname: Csordas
authors.forename: José A
authors.initials: JA
authors.lastname: Dianes
authors.forename: Antonio
authors.initials: A
authors.lastname: Fabregat
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Foster
authors.forename: Johannes
authors.initials: J
authors.lastname: Griss
authors.forename: Emanuele
authors.initials: E
authors.lastname: Alpi
authors.forename: Melih
authors.initials: M
authors.lastname: Birim
authors.forename: Javier
authors.initials: J
authors.lastname: Contell
authors.forename: Gavin
authors.initials: G
authors.lastname: O'Kelly
authors.forename: Andreas
authors.initials: A
authors.lastname: Schoenegger
authors.forename: David
authors.initials: D
authors.lastname: Ovelleiro
authors.forename: Yasset
authors.initials: Y
authors.lastname: Pérez-Riverol
authors.forename: Florian
authors.initials: F
authors.lastname: Reisinger
authors.forename: Daniel
authors.initials: D
authors.lastname: Ríos
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.forename: Henning
authors.initials: H
authors.lastname: Hermjakob
mesh_terms: D030562:Databases, Protein; D020407:Internet; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D040901:Proteomics; D012984:Software
chemical_list: D010455:Peptides; D011506:Proteins