Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

Frank Desiere^*¹^,2 , Eric W Deutsch^*² , Alexey I Nesvizhskii^*² , Parag Mallick^*² , Nichole L King² , Jimmy K Eng² , Alan Aderem² , Rose Boyle², Erich Brunner²^,3, Samuel Donohoe² , Nelson Fausto⁴, Ernst Hafen³, Lee Hood² , Michael G Katze⁵, Kathleen A Kennedy² , Floyd Kregenow² , Hookeun Lee² , Biaoyang Lin² , Dan Martin² , Jeffrey A Ranish² , David J Rawlings⁶, Lawrence E Samelson⁷, Yuzuru Shiio² , Julian D Watts² , Bernd Wollscheid² , Michael E Wright² , Wei Yan² , Lihong Yang⁸, Eugene C Yi² , Hui Zhang² and Ruedi Aebersold²^,9

¹Nestlé Research Center, 1000 Lausanne 26, Switzerland

²Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA

³Institute of Zoology, University of Zürich, CH-8057 Zürich, Switzerland

⁴Department of Pathology, University of Washington, Seattle, WA 98195-7705, USA

⁵Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 98195, USA

⁶Department of Pediatrics, University of Washington, Seattle, WA 98195, USA

⁷National Cancer Institute, 37 Convent Drive, Bethesda, MD 20892, USA

⁸North Shore Long Island Jewish Research Institute, 350 Community Drive, Manhasset, NY 11030, USA

⁹Institute of Biotechnology, Swiss Federal Institute of Technology, ETH Hönggerberg, HPT E 78, CH-8093 Zürich, Switzerland

author email corresponding author email* Contributed equally

Genome Biology 2004, 6:R9doi:10.1186/gb-2004-6-1-r9


Published:	10 December 2004

Subject areas: Genome studies, Biochemistry and structural biology, Methods

Abstract

A crucial aim upon the completion of the human genome is the verification and functional annotation of all predicted genes and their protein products. Here we describe the mapping of peptides derived from accurate interpretations of protein tandem mass spectrometry (MS) data to eukaryotic genomes and the generation of an expandable resource for integration of data from many diverse proteomics experiments. Furthermore, we demonstrate that peptide identifications obtained from high-throughput proteomics can be integrated on a large scale with the human genome. This resource could serve as an expandable repository for MS-derived proteome information.