This chapter examines the role of capillary electrophoresis (CE) in the separation of tropane alkaloids, glycoalkaloids, and closely related compounds that have either pharmaceutical value or toxicological effects on humans. The latest significant developments in CE analysis have been selected and critically discussed. When the conventional CE mode was found unable to provide an acceptable selectivity towards the analytes, the addition of either an organic solvent, a chiral selector, or a surfactant to the running buffers was exploited. Likewise, nonaqueous CE (NACE) was also employed to increase solute solubilities and for a better compatibility of this media with mass spectrometry. It turns out that, upon selecting the most appropriate experimental conditions, the CE separation of tropane alkaloids and steroidal glycoalkaloids of Solanaceae plants was successfully accomplished. All major steps involved in the separation and detection of these secondary metabolites in complex samples are described and the relevant aspects of each application are examined with emphasis on the main aspects entailed a typical assay. More applications have yet to be developed in order to encourage more labs to exploit the tremendous potential of capillary electrophoresis.
