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. 2010 Jan;38(Database issue):D736-42.
doi: 10.1093/nar/gkp964. Epub 2009 Nov 11.

The Proteomics Identifications database: 2010 update

Juan Antonio Vizcaíno  1 , Richard Côté, Florian Reisinger, Harald Barsnes, Joseph M Foster, Jonathan Rameseder, Henning Hermjakob, Lennart Martens
Affiliations

The Proteomics Identifications database: 2010 update

Juan Antonio Vizcaíno et al. Nucleic Acids Res. 2010 Jan.

Abstract

The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 million spectra by September 2009. We here describe several new and improved features in PRIDE, including the revised submission process, which now includes direct submission of fragment ion annotations. Correspondingly, it is now possible to visualize spectrum fragmentation annotations on tandem mass spectra, a key feature for compliance with journal data submission requirements. We also describe recent developments in the PRIDE BioMart interface, which now allows integrative queries that can join PRIDE data to a growing number of biological resources such as Reactome, Ensembl, InterPro and UniProt. This ability to perform extremely powerful across-domain queries will certainly be a cornerstone of future bioinformatics analyses. Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium.

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Figures

Figure 1.
Figure 1.
Growth of data content in PRIDE from September 2007 until September 2009. The data included in the graph are number of spectra, protein identifications, peptide identifications and unique peptides.
Figure 2.
Figure 2.
Screenshot showing spectrum fragmentation annotation on tandem mass spectra as visualized in the ‘PRIDE Spectrum Viewer’. Y ions are highlighted in red, B ions in blue and neutral loss ions in green.
Figure 3.
Figure 3.
Screenshot showing the opening frame of PRIDE Converter. It allows the user to choose the appropriate format from the list of supported software-specific formats that can be converted into PRIDE XML.
See this image and copyright information in PMC

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