NAR Molecular Biology Database Collection entry number 851
Desiere F., Deutsch E.W., King N.L., Nesvizhskii A.I, Mallick P., Eng J., Chen S., Eddes J., Loevenich S.N., and Aebersold R.
Institute for Systems Biology, Seattle, WA

Database Description

The PeptideAtlas (1) is a multi-organism, publicly accessible compendium of peptides identified in a large set of LC-MS/MS proteomics experiments. Some of the experimental data have been already published; many are still unpublished. All results of sequence searching have subsequently been processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner to insure a high quality database. All peptides have been mapped to Ensembl and can be viewed as custom tracks on the Ensembl Genome Browser.

The PeptideAtlas will continue to grow as more datasets and organisms are added. We welcome data submissions, which we will incorporate into the atlas.

Recent Developments

PeptideAtlas is a first step towards the goal of fully annotating and validating eukaryotic genomes by using experimentally observed protein-products. PeptideAtlas provides a process and a framework to accommodate proteome information generated by high-throughput proteomics technologies and is able to efficiently disseminate experimental data in the public domain. Its significance continues to grow as more data are submitted from diverse experiments, using different cellular compartments and enrichments methods. PeptideAtlas also provides a resource for the development of new avenues of research. The datasets will provide a rich source of data for computational scientists to develop and test new algorithms for proteomic analysis, gene-discovery and splice variant prediction. The need for public proteomics data repositories is recognized (3) and we intend PeptideAtlas to continue to grow as a public database and resource. We strongly encourage researchers to contribute their own MS/MS data to the PeptideAtlas project. In the near future, we will make builds for organisms such as mouse, Arabidopsis thaliana and Halobacterium sp. NRC-1, and continue to make subsets such as the Human Plasma PeptideAtlas (2). Also in the near future we hope to provide an interface to access representative spectra of peptides, and will provide a way to retrieve information on peptide modifications (such as phosphorylation, etc.).


1. Desiere,F., Deutsch,E.W., Nesvizhskii,A.I., Mallick,P., King,N.L., Eng,J.K., Aderem,A., Boyle,R., Brunner,E., Donohoe,S. et al. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol., 6, R9.
2. Deutsch,E.W., Eng,J.K., Zhang,H., King,N.L., Nesvizhskii,A.I., Lin,B., Lee,H., Yi,E.C., Osssola,R. and Aebersold,R. (2005) Human Plasma PeptideAtlas. Proteomics., 5.
3. Prince,J.T., Carlson,M.W., Wang,R., Lu,P. and Marcotte,E.M. (2004) The need for a public proteomics repository. Nat Biotechnol, 22, 471-472.

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