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

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

2013, Vol. 41, Database issue | Juan Antonio Vizcaíno1*, Richard G. Côté1, Attila Csordas1, José A. Dianes1, Antonio Fabregat1, Joseph M. Foster1, Johannes Griss1, Emanuele Alpi1, Melih Birim1, Javier Contell1, Gavin O'Kelly1, Andreas Schoenegger1,3, David Ovelleiro1, Yasset Pérez-Riverol1,2, Florian Reisinger1, Daniel Ríos1, Rui Wang1 and Henning Hermjakob1
The PRoteomics IDentifications (PRIDE) database, hosted by the European Bioinformatics Institute, is a prominent repository for mass spectrometry (MS)-based proteomics data. This article provides an update on recent developments in PRIDE and related tools. It highlights the increase in data content, including the number of experiments, identified proteins, peptides, and spectra. The article details the PRIDE submission process, emphasizing the new PRIDE Converter 2 tool for data conversion and the PRIDE Inspector for data visualization and quality assessment. It also discusses the integration of PRIDE with other MS proteomics resources through the ProteomeXchange consortium and ongoing quality control efforts. Future plans include the development of a new resource, PRIDE-Q, for quality-controlled data and the continued support for PSI standards. The article underscores PRIDE's role in facilitating data sharing and analysis in the proteomics community.The PRoteomics IDentifications (PRIDE) database, hosted by the European Bioinformatics Institute, is a prominent repository for mass spectrometry (MS)-based proteomics data. This article provides an update on recent developments in PRIDE and related tools. It highlights the increase in data content, including the number of experiments, identified proteins, peptides, and spectra. The article details the PRIDE submission process, emphasizing the new PRIDE Converter 2 tool for data conversion and the PRIDE Inspector for data visualization and quality assessment. It also discusses the integration of PRIDE with other MS proteomics resources through the ProteomeXchange consortium and ongoing quality control efforts. Future plans include the development of a new resource, PRIDE-Q, for quality-controlled data and the continued support for PSI standards. The article underscores PRIDE's role in facilitating data sharing and analysis in the proteomics community.
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