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Oxford University Press, Nucleic Acids Research, D1(41), p. D1063-D1069, 2012

DOI: 10.1093/nar/gks1262

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

Journal article published in 2012 by Juan Antonio Vizcaíno ORCID, Richard G. Côté, R. G. Cote, Attila Csordas, José A. Dianes, Antonio Fabregat ORCID, Joseph M. Foster, Johannes Griss ORCID, Emanuele Alpi, Melih Birim, Javier Contell, Gavin O'Kelly, Gavin O’Kelly, Andreas Schoenegger, David Ovelleiro and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.