This chapter presents the technique of capillary electrophoresis coupled to mass spectrometry (CE/MS). The introductory section is targeted mainly at CE/MS beginners and notes briefly the theoretical background of electrospray ionization (ESI), the most commonly used ionization mode in CE/MS. The specifics of CE/MS are described—also in comparison with more classic methods like LC/MS. Important caveats to be taken nto consideration for successful CE/MS operation are noted in the interest of avoiding pitfalls. CE/MS is illustrated with three representative examples, which might serve as starting points for more in-detail experiments: (1)partial-fillingmicellar elektrokinetic chromatography (MEKC) ofneutralbacterial signaling molecules (N-acylhomoserine lactones) extracted from culture supernatants, (2) capillary zone electrophoresis (CZE) of their anionic degradation products, and finally (3) CZE separation ofcationichydroxys-triazines.
