Separation in capillary electrophoresis (CE) is based on the movement of charged compounds inside a background electrolyte under an applied potential. Because the mechanism of separation of CE differs from that of conventional high-performance liquid chromatography (HPLC), where separation is based on the analyte’s hydrophobic properties, CE is often used as a complementary technique to HPLC. In addition, because CE is performed in narrow capillaries at atmospheric pressure, it is used as an alternative to HPLC, capable of handling small sample volumes while providing shorter analysis times with higher efficiency. For the analysis of amino acid, protein, and peptide mixtures in small volume samples such as in single cells, CE has rapidly evolved as a preferred separation technique. The combination of a high-efficiency separation technique, such as CE, with mass spectrometry (MS) detection provides a powerful system for the analysis of complex biological mixtures. In this chapter, a theoretical and practical approach to achieving high-performance CE-MS is discussed and the utility of CE-MS for the analysis of amino acids, peptides, and proteins is demonstrated.
