Capillary electrophoresis-mass spectrometry of peptides from enzymatic protein hydrolysis: simulation and optimization.

Two important limitations still exist for the characterization of protein digests by capillary electrophoresis-mass spectrometry (CE-MS): (i) the buffer choice (i.e., the buffer must provide an adequate CE separation without ruining the MS signal), and (ii) the frequent generation of "unexpected" peptidic fragments during the enzymatic protein hydrolysis. In this work, a new approach is used to solve these difficulties, namely a theoretical model that relates the electrophoretic behavior of peptides to their sequence. The effectiveness of this procedure is demonstrated by the fast attainment of good CE-MS conditions for analyzing the peptides obtained from an enzymatic protein hydrolysate in a single run. This strategy can provide useful information for helping to characterize "unexpected" fragments from protein digests.