Analysis of the Mouse Liver Proteome Using Advanced Mass Spectrometry

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