Method
A mouse plasma peptide atlas as a resource for disease proteomics
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* Corresponding author: Qing Zhang qing@fhcrc.org
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
Genome Biology 2008, 9:R93 doi:10.1186/gb-2008-9-6-r93
Published: 3 June 2008Abstract
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.