INTRODUCTION: Mass spectrometric analysis of intact protein bacterial lysates generates unique protein expression profiles for bacterial strain differentiation. The greater information content afforded to electrospray ionization makes LCMS preferable to MALDI when differentiating at a serovar or strain level. Advances in protein chromatography and LCMS compatible deconvolution software make it possible to generate reproducible accurate mass profiles specific to a given serovar. However, prior experiments have shown that many chromatographically resolved proteins are not being detected. In our current work we investigate whether the same chromatographic separation on higher resolving power and higher sensitivity instruments reveals lower abundant proteins that are currently being missed. In addition, differences in electrospray ionization sources being employed offer varying improvements in sensitivity.