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

Frank Desiere12, Eric W Deutsch2, Alexey I Nesvizhskii2, Parag Mallick2, Nichole L King2, Jimmy K Eng2, Alan Aderem2, Rose Boyle2, Erich Brunner23, 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 Aebersold29*

Author Affiliations

1 Nestlé Research Center, 1000 Lausanne 26, Switzerland

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

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

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

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

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

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

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

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

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Genome Biology 2004, 6:R9  doi:10.1186/gb-2004-6-1-r9

Published: 10 December 2004

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.