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Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

Nichole L King1*, Eric W Deutsch1, Jeffrey A Ranish1, Alexey I Nesvizhskii2, James S Eddes1, Parag Mallick3, Jimmy Eng14, Frank Desiere5, Mark Flory6, Daniel B Martin17, Bong Kim1, Hookeun Lee8, Brian Raught9 and Ruedi Aebersold18

Author Affiliations

1 Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA

2 Department of Pathology, University of Michigan, Catherine Road, Ann Arbor, MI 48109, USA

3 Louis Warschaw Prostate Cancer Center, Cedars-Sinai Medical Center, W. Third St, Los Angeles, CA 90048, USA

4 PHSD, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

5 Nestlé Research Center, 1000 Lausanne 26, Switzerland

6 Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA

7 Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA

8 IMSB, ETH Zurich and Faculty of Science, University of Zurich, Zurich, Switzerland

9 University Health Network, Ontario Cancer Institute and McLaughlin Centre for Molecular Medicine, College Street, Toronto, ON M5G 1L7, Canada

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Genome Biology 2006, 7:R106  doi:10.1186/gb-2006-7-11-r106

Published: 13 November 2006

Abstract

We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.