pubmed.ncbi.nlm.nih.gov

PRIDE: new developments and new datasets - PubMed

  • ️Invalid Date

. 2008 Jan;36(Database issue):D878-83.

doi: 10.1093/nar/gkm1021. Epub 2007 Nov 22.

Affiliations

PRIDE: new developments and new datasets

Philip Jones et al. Nucleic Acids Res. 2008 Jan.

Abstract

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.

PRIDE includes data for 25 different species. This pie chart illustrates the representation of each species in terms of the total number of peptide identifications for each species.

Figure 2.
Figure 2.

This graph illustrates the increasing redundancy of the peptide identifications submitted to PRIDE over the last year, as repeated identifications of the same peptides are performed. The total number of peptide identifications has increased 5.5-fold, however the number of unique peptide identifications in PRIDE has only doubled.

Figure 3.
Figure 3.

A single sheet from the ProteomeHarvest PRIDE Submission Spreadsheet—Peptide Identification Data Entry.

Figure 4.
Figure 4.

The PRIDE BioMart: results summary view for a simple query. The filter and display attributes can be seen on the left.

Similar articles

Cited by

References

    1. Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R. Pride: the proteomics identifications database. Proteomics. 2005;5:3537–3545. - PubMed
    1. Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R. Pride: a public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 2006;34:D659–D663. - PMC - PubMed
    1. Mead JA, Shadforth IP, Bessant C. Public proteomic ms repositories and pipelines: available tools and biological applications. Proteomics. 2007;7:2769–2786. - PubMed
    1. Editorial. Democratizing proteomics data. Nat. Biotechnol. 2007;25:262. - PubMed
    1. Craig R, Cortens JC, Fenyo D, Beavis RC. Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 2006;5:1843–1849. - PubMed

Publication types

MeSH terms

Substances