Liquid-phase separation techniques such as liquid chromatography (LC) or capillary electrophoresis (CE) coupled with mass spectrometry is essential for high throughput / high sensitivity analysis of complex proteomic mixtures. CE offers high efficiency separations, low sample consumption, as well as peptide compositional information. Two-dimensional display of CE-MS data yields distinct charge-based trends for the logarithm of the effective electrophoretic mobility (μeff) versus the logarithm of the measured peptide [M + H]+ values (See Figure 1).1 These charge-based trends provide analytical utility for protein identification. For example, peptides similar in mass but different in basic amino acid composition can be easily identified. In Figure 1, two E. coli derived peptides, ADLNVPVKDGK (m/z 1155.626) and ASLPTIELALK (m/z 1155.698) denoted as A and B, respectively, were identified using this approach. Overall, these charge-based trends provide specific utility toward detecting peptides with charge altering modifications (i.e., phosphorylation, sulfation, etc.), similar in mass, and peptides with insufficient tandem MS data.