From Peptidome to PRIDE: public proteomics data migration at a large scale

Abstract

The PRIDE database, developed and maintained at the European Bioinformatics Institute (EBI), is one of the most prominent data repositories dedicated to high throughput MS-based proteomics data. Peptidome, developed by the National Center for Biotechnology Information (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 Peptidome 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 Peptidome 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.