RP-HPLC prefractionation and its application in expressional proteomics analysis of an in vitro viral infection model.

Prefractionation of complex protein mixtures is an efficient method for increasing the separation power of 2-DE. RP-HPLC has been successfully utilized as a prefractionation method prior to 2-DE. Here we describe the optimization of an efficient RP-HPLC method for prefractionation of baby hamster kidney cell solubilized proteins. A step gradient elution of acetonitrile was optimized and collected fractions were further examined by SDS-PAGE and 2-DE. By utilizing this method an effective increase in separation power of 2-DE is accomplished. Moreover, we describe the application of this method to expressional proteome analysis of a virally infected cell model.