PRIDE: new developments and new datasets.
The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML.
Jones
Philip
P
EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. pjones@ebi.ac.uk
Côté
Richard G
RG
Cho
Sang Yun
SY
Klie
Sebastian
S
Martens
Lennart
L
Quinn
Antony F
AF
Thorneycroft
David
D
Hermjakob
Henning
H
D000818:Animals; D030562:Databases, Protein; D020407:Internet; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics; D014584:User-Computer Interface
D010455:Peptides; D011506:Proteins