An automated method is described to measure tracer-tracee-ratios (TTR) of plasma amino acids after their separation as 9-fluorenylmethylchloroformate derivatives. In a 45 min cycle, 5 microl plasma aliquots were derivatized, HPLC separated and subjected to electrospray ionization. By applying source collision induced dissociation, derivatives were dissociated at the peptide bond releasing the originating amino acids into the mass spectrometer. This approach enabled the determination of plasma amino acid TTRs with a standard deviation between 0.15 and 0.36%, which is sufficient to study the fate of infused tracers and their conversion products in an in vivo experiment in humans.