Open Access Highly Accessed Open Badges Method

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

For all author emails, please log on.

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

Published: 3 June 2008


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.