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MPI für Biochemie  

Proteomics and Signal Transduction
Matthias Mann

Analysis of the Mouse Liver Proteome Using Advanced Mass Spectrometry

 


J Proteome Res. 2007 Jul 3; [Epub ahead of print]

Analysis of the Mouse Liver Proteome Using Advanced Mass Spectrometry.

Shi R, Kumar C, Zougman A, Zhang Y, Podtelejnikov A, Cox J, Wiśniewski JR, Mann M.


Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China, and Proxeon Biosystems A/S, Stærmosegårdsvej 6, 5230 Odense, Denmark.

 

We report a large-scale analysis of mouse liver tissue comprising a novel fractionation approach and high-accuracy mass spectrometry techniques. Two fractions enriched for soluble and membrane proteins from 20 mg of frozen tissue were separated by one-dimensional electrophoresis followed by LC-MS/MS on the hybrid linear ion trap (LTQ)-Orbitrap mass spectrometer. Confident identification of 2210 proteins relied on at least two peptides. We combined this proteome with our previously reported organellar map (Foster et al. Cell 2006, 125, 187-199) to generate a very high confidence mouse liver proteome of 3244 proteins. The identified proteins represent the liver proteome with no discernible bias due to protein physicochemical properties, subcellular distribution, or biological function. Forty-seven percent of identified proteins were annotated as membrane-bound, and for 35.3%, transmembrane domains were predicted. For potential application in toxicology or clinical studies, we demonstrate that it is possible to consistently identify more than 1000 proteins in a single run. Keywords: liver * LC-MS/MS * LTQ-Orbitrap * toxicology * 2D gel electrophoresis * proteomics.