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.
Keywords: Rat liver • Proteome map • 2-D PAGE • Pre-fractionation • MALDI-TOF/TOF