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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 DePinho45, Nabeel Bardeesy6, Daniela Dinulescu7, Kenneth E Hung6, Raju Kucherlapati6, Tyler Jacks8, Katerina Politi9, Ruedi Aebersold103, Gilbert S Omenn2, David J States2 and Samir M Hanash1

Author Affiliations

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

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

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

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

5 Center 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

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

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

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

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

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

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Genome Biology 2008, 9:R93  doi:10.1186/gb-2008-9-6-r93

Published: 3 June 2008

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.