The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

Juan Antonio Vizcaíno(Austrian Academy of Sciences), Richard G. Côté(CeMM Research Center for Molecular Medicine), Attila Csordás(European Bioinformatics Institute), José A. Dianes(CeMM Research Center for Molecular Medicine), Antonio Fabregat(European Bioinformatics Institute), Joseph Foster(Austrian Academy of Sciences), Johannes Griss(Wellcome Trust), Emanuele Alpi(CeMM Research Center for Molecular Medicine), Melih Birim(Centro de Ingeniería Genética y Biotecnología), Javier Contell(Wellcome Trust), Gavin O’Kelly(European Bioinformatics Institute), Andreas Schoenegger(CeMM Research Center for Molecular Medicine), David Ovelleiro(Centro de Ingeniería Genética y Biotecnología), Yasset Pérez‐Riverol(CeMM Research Center for Molecular Medicine), Florian Reisinger(Wellcome Trust), Daniel Ríos(CeMM Research Center for Molecular Medicine), Rui Wang(Wellcome Trust), Henning Hermjakob(Wellcome Trust)
Nucleic Acids Research
November 29, 2012
10.1093/nar/gks1262
Cited by 1,964Open Access
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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.

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