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The PeptideAtlas project
1Institute for Systems Biology Seattle, WA, USA 2Cedars-Sinai Medical Center Los Angeles, CA, USA 3UCLA Department of Chemistry and Biochemistry Los Angeles, CA, USA 4Public Health Sciences Division, Fred Hutchinson Cancer Research Center Seattle, WA, USA 5Institute of Zoology, University of Zurich Winterthurstrasse 190, 8057 Zürich, Switzerland 6Institute of Molecular Systems Biology, Swiss Federal Institute of Technology ETH Hönggerberg, Zürich, Switzerland 7Nestlé Research Center, Vers-chez-les-Blanc 1026 Lausanne, Switzerland
*To whom correspondence should be addressed. Email: fdesiere{at}yahoo.com; frank.desiere{at}rdls.nestle.com
Received August 4, 2005. Revised October 3, 2005. Accepted October 3, 2005.
The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. PeptideAtlas (http://www.peptideatlas.org/) addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.
The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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