Comparison of mobilities of peptides and proteins by capillary electrophoresis and ion mobility coupled to mass spectrometry

Abstract

Native mass spectrometry (nMS) coupled to ion mobility (IM-MS) is an analytical strategy for studying biological systems, particularly proteins and peptides, after transferring them to the gas phase. However, can the absence of certain interactions in the gas phase compared to those in solution result in new conformations compared to their native states? Or are ionic conformations kinetically trapped? The aim of this work is to provide some answers to these questions by studying peptides obtained following trypsin digestion of a well-known protein, bovine serum albumin. The peptides derived from this digestion were studied using two separation methods, one in the gas phase (ion mobility) coupled with another in solution (capillary electrophoresis), which also provided information on the structural parameters of the systems studied. Both methods were tested under different conditions (pH, interface between the two methods, ion activation regime) to determine the influence of experimental parameters. After analysis and interpretation of the results, it was found that despite similar conformational distributions between the two phases for the majority of peptides. Some peptides undergo conformational changes after desolvation.