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The PeptideAtlas Project

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The PeptideAtlas Project

Eric W Deutsch. Methods Mol Biol.

Abstract

PeptideAtlas is a multi-species compendium of peptides observed with tandem mass spectrometry methods. Raw mass spectrometer output files are collected from the community and reprocessed through a uniform analysis and validation pipeline that continues to advance. The results are loaded into a database and the information derived from the raw data is returned to the community via several web-based data exploration tools. The PeptideAtlas resource is useful for experiment planning, improving genome annotation, and other data mining projects. PeptideAtlas has become especially useful for planning targeted proteomics experiments.

Figures

Figure 1
Figure 1
An overview of the build process of PeptideAtlas. Shotgun tandem mass spectrometry (MS/MS) experimental data are contributed by the community to the PeptideAtlas raw data repository, which is linked to other repositories via the ProteomExchange consortium. The raw data are processed through an evolving but consistent analysis and validation pipeline (Trans Proteomic Pipeline (TPP)) and loaded into the PeptideAtlas database, and made available to the community. Tranche, GPMDB (Global Proteome Machine Database), NIST (National Institute of Standards and Technology), and PRIDE (Protein Identifications Database) are the current major participants in the ProteomExchange consortium.
Figure 2
Figure 2
Cytoscape visualization of a simple set of proteins and peptides. The 2 proteins are drawn as purple oval nodes. Peptides are drawn as rectangular nodes. Edges indicate the mapping of peptides to proteins. Peptides that have only one edge are uniquely mapping; peptides with two or more edges are ambiguously mapped. Peptide rectangle borders become thicker and redder with greater numbers of observations. Proteotypic peptides (uniquely mapping, multiply observed, and having EOS > 0.3) are shaded in green.

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