Application of capillary electrophoresis/ electrospray ionization-mass spectrometry to subcellular proteomics of Escherichia coli ribosomal proteins

We introduce capillary electrophoresis-mass spectrometry (CE-MS) as an efficient means for the on-line separation and identification of protein mixtures. It was found that while CE/electrospray ionization (ESI)-MS analysis of whole-cell lysate was too complicated for the one-dimensional CE-MS analysis, the technique was useful for the analysis of protein mixtures of moderate complexity (∼50 intact proteins). CE/ESI-MS was applied to the subcellular proteomics of ribosomal Escherichia coli. 55 out of the 56 ribosomal proteins were detected with ease by using only ∼3.4 ng of ribosomal proteins. In addition, it was found that the mass accuracy of the conventional MS (such as quadrupole ion traps) was good enough to identify many post-translational modifications of the intact proteins by simply comparing their measured average molecular weight with the average molecular weight predicted from gene banks.