NCBI Peptidome: a new repository for mass spectrometry proteomics data

Abstract

Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Data from all stages of a mass spectrometry experiment are captured, including original mass spectra files, experimental metadata and conclusion-level results. The submission process is facilitated through acceptance of data in commonly used open formats, and all submissions undergo syntactic validation and curation in an effort to uphold data integrity and quality. Peptidome is not restricted to specific organisms, instruments or experiment types; data from any tandem mass spectrometry experiment from any species are accepted. In addition to data storage, web-based interfaces are available to help users query, browse and explore individual peptides, proteins or entire Samples and Studies. Results are integrated and linked with other NCBI resources to ensure dissemination of the information beyond the mass spectroscopy proteomics community. Peptidome is freely accessible at http://www.ncbi.nlm.nih.gov/peptidome.

Figure 1.

A schematic overview of Peptidome. The main logical entity is a ‘Study’ which contains a set of related ‘Samples’. Each Sample contains a list of both identified ‘proteins’ and ‘peptides’. Proteins contain links to their member peptides, and peptides know which proteins they are members of. Furthermore, peptides are linked to individual ‘spectra’ through peptide identifications (pepIdents), thus allowing more than one interpretation of a spectrum, and providing storage for post-translational modifications and identification scores.

Figure 2.

A series of screenshots showing navigation from a top level list of Studies (1), to its list of Samples (2), to the protein list for a Sample (3), to the list of peptide identifications for that protein (4) and finally to three individual spectra for different peptide identifications (5).