The Proteomics Identifications database: 2010 update
Author(s)
Vizcaino, Juan Antonio; Cote, Richard; Reisinger, Florian; Barsnes, Harald; Foster, Joseph M.; Rameseder, Jonathan; Hermjakob, Henning; Martens, Lennart; ... Show more Show less
DownloadVizcaino-2009-The Proteomics Identifications database.pdf (3.098Mb)
PUBLISHER_CC
Publisher with Creative Commons License
Creative Commons Attribution
Terms of use
Metadata
Show full item recordAbstract
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.
Date issued
2009-11Department
Massachusetts Institute of Technology. Computational and Systems Biology ProgramJournal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Vizcaino, J. A. et al. “The Proteomics Identifications Database: 2010 Update.” Nucleic Acids Research 38.Database (2009): D736–D742. Web.
Version: Final published version
ISSN
0305-1048
1362-4962