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

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ID: 291069
2012
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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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Authors Juan Antonio Vizcaíno, Richard G. Côté, Attila Csordás, José A. Dianes, Antonio Fabregat, Joseph Foster, Johannes Griss, Emanuele Alpi, Melih Birim, Javier Contell, Gavin O’Kelly, Andreas Schoenegger, David Ovelleiro, Yasset Pérez‐Riverol, Florian Reisinger, Daniel Ríos, Rui Wang, Henning Hermjakob
Journal Nucleic Acids Research
Year 2012
DOI
10.1093/nar/gks1262
URL
https://academic.oup.com/nar/article-pdf/41/D1/D1063/3711170/gks1262.pdf
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