Biology Reference
In-Depth Information
4.2.2. Proteomics repositories
The HUPO PSI is also closely related to the development of the
PRoteomics IDEntifications database (PRIDE). PRIDE was put
together to provide the proteomics community with a public repository
for protein and peptide identifications together with the evidence sup-
porting these identifications.
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PRIDE is a centralized, standards-compliant,
public data repository for proteomics data. Each entry in the database
contains the proteins identified, a list of peptides used to make identifi-
cations, the tissue, the experiment conducted, the conditions of the
experiment, any PTMs to those peptides, and links to any publication
describing the experiment. PRIDE has a dual objective: it is designed to
provide (1) a common data exchange format and repository to support
proteomics literature publications, and (2) a reference set of tissue-based
identifications for use by the community.
PeptideAtlas
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was designed to store proteomics data generated by
high-throughput methods. It is actually presented as an expandable
resource for integration of data from diverse proteomics experiments.
This initiative is driven by the assumption that protein expression data
can contribute to the annotation of eukaryotic genomes. MS/MS spec-
tra are stored in the PeptideAtlas database. Each statistically validated
assignment of a peptide to a mass spectrum is recorded. A range of con-
fidence thresholds is optionally made available for selecting peptides
likely to match proteins, and false-positive rates are correspondingly esti-
mated. A database scheme supports different builds of PeptideAtlas, sev-
eral versions of Ensembl, a range of eukaryotic organisms, and several
reference protein sequence sets. PeptideAtlas currently includes data pro-
duced at the ISB, which hosts the resource. As it is intended as a data
repository, a large set of published data are also available for download.
The Global Proteome Machine (GPM)
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is another similar approach
to storing MS/MS data. The GPM database is used on its own, to pro-
vide answers to specific queries, as well as to serve as an index to exper-
imental information stored in XML documents. The underlying schema
serves as both an extension and a simplification of the MIAPE idea, for
the purpose of validating observed protein coverage and peptide frag-
mentation data.
