Improved method for proteome mapping of the liver by 2-DE MALDI-TOF MS

Identifying the liver proteome has been the subject of intensified research. Notably, due to their strong heterogeneity in size, charge, solubility, and relative abundance, different strategies of pre-fractionation must be employed to increase the number of identifiable proteins. In our efforts, we used two different lysis buffers in sequence, a liquid-phase IEF pre-fractionation and separation of protein mixtures at three different pH ranges (3-10, 5-8, and 7-10). Then, > 15 000 gel digested proteins were investigated. We report an identification of 590 different gene products, including some isoforms. More than 150 proteins have not been reported so far by two-dimensional electrophoresis (2-DE) proteome mapping. We further studied the transcript expression of more than 33 000 genes in rat liver to explore correlations between transcript and protein expression. Overall, we report a method for the separation of rat liver proteins and their identification by mass spectrometry. The newly identified proteins will enable an improved understanding of liver biology.