A mouse plasma peptide atlas as a resource for disease proteomics

Qing Zhang¹ , Rajasree Menon² , Eric W Deutsch³ , Sharon J Pitteri¹ , Vitor M Faca¹ , Hong Wang¹ , Lisa F Newcomb¹ , Ronald A DePinho⁴^,5 , Nabeel Bardeesy⁶ , Daniela Dinulescu⁷ , Kenneth E Hung⁶ , Raju Kucherlapati⁶ , Tyler Jacks⁸ , Katerina Politi⁹ , Ruedi Aebersold³^,10 , Gilbert S Omenn² , David J States² and Samir M Hanash¹

¹Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA

²Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA

³Institute for Systems Biology, Seattle, WA 98103, USA

⁴Dana-Farber Cancer Institute, Harvard Cancer Center, Boston, MA 02115, USA

⁵Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Department of Medical Oncology, Medicine, Genetics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02114, USA

⁶Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA

⁷Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA

⁸Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

⁹Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA

¹⁰Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, 8093 Zurich, Switzerland

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Genome Biology 2008, 9:R93doi:10.1186/gb-2008-9-6-r93


Published:	3 June 2008

Subject areas: Genome studies, Methods, Model organisms

Abstract

We present an in-depth analysis of mouse plasma leading to the development of a publicly available repository composed of 568 liquid chromatography-tandem mass spectrometry runs. A total of 13,779 distinct peptides have been identified with high confidence. The corresponding approximately 3,000 proteins are estimated to span a 7 logarithmic range of abundance in plasma. A major finding from this study is the identification of novel isoforms and transcript variants not previously predicted from genome analysis.