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 Eng¹^,4 , Frank Desiere⁵ , Mark Flory⁶ , Daniel B Martin¹^,7 , Bong Kim¹ , Hookeun Lee⁸ , Brian Raught⁹ and Ruedi Aebersold¹^,8

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

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

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

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

⁵Nestlé Research Center, 1000 Lausanne 26, Switzerland

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

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

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

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

author email corresponding author email

Genome Biology 2006, 7:R106doi:10.1186/gb-2006-7-11-r106


Published:	13 November 2006

Subject areas: Biochemistry and structural biology, Bioinformatics

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.