Capillary zone electrophoresis is employed for the separation and analysis of both fluorescein thiohydantoin and dimethylaminoazobenzene thiohydantoin derivatives of amino acids. Detection of minute amounts of these amino acid derivatives is an important milestone in the development of a high sensitivity protein sequencer. Current detection limits for the fluorescein derivative is on the order of 10(-21) moles whereas detection limits for the dimethylaminoazobenzene derivative is on the order of 10(-16) moles.