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From Peptidome to PRIDE : P ublic proteomics data migration at a large scale
Author(s) -
Csordas Attila,
Wang Rui,
Ríos Daniel,
Reisinger Florian,
Foster Joseph M.,
Slotta Douglas J.,
Vizcaíno Juan Antonio,
Hermjakob Henning
Publication year - 2013
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201200514
Subject(s) - pride , proteomics , computer science , proteogenomics , database , biology , genomics , genome , genetics , political science , gene , law
The PRIDE database, developed and maintained at the E uropean B ioinformatics I nstitute (EBI), is one of the most prominent data repositories dedicated to high throughput MS ‐based proteomics data. Peptidome, developed by the N ational C enter for B iotechnology I nformation ( NCBI ) as a sibling resource to PRIDE , was discontinued due to funding constraints in April 2011. A joint effort between the two teams was started soon after the P eptidome closure to ensure that data were not “lost” to the wider proteomics community by exporting it to PRIDE . As a result, data in the low terabyte range have been migrated from P eptidome to PRIDE and made publicly available under experiment accessions 17 900–18 271, representing 54 projects, ∼53 million mass spectra, ∼10 million peptide identifications, ∼650 000 protein identifications, ∼1.1 million biologically relevant protein modifications, and 28 species, from more than 30 different labs.