An electrospray ionization (ESI) source was used to generate gas-phase molecular anions of the amino acids leucine and isoleucine ((M–H) −; m/z −130), which were separated by high- field asymmetric waveform ion mobility spectrometry (FAIMS) and detected by quadrupole mass spectrometry (MS). This combination of ESI-FAIMS-MS enabled selective determination of either amino acid in mixtures that contained at least a 625-fold excess of the other. Comparisons with conventional ESI-MS showed a 50-fold improvement in the signal to background ratio for a 1 μM solution of leucine.