Lithium cation complexes with cysteine (Cys) are collisionally activated with xenon in a guided ion beam tandem mass spectrometer and observed to deaminate in addition to loss of the intact amino acid. Source conditions are found to influence the cross sections for these processes considerably, a result interpreted in terms of two isomers, Li+(Cys) and (NH3)Li+(C3H4O2S). Quantum chemical calculations at the B3LYP/6-311G(d,p) level are used to explore the reaction mechanism for this fragmentation process in detail. A complete reaction coordinate surface for the process is elucidated, including all intermediates and transition states. Theoretical molecular parameters for the two isomers and for file rate-limiting transition state for deamination of Li+ (CYS) are thell used to analyze the threshold energies in the experimental data, providing experimental measurements of the energies of the transition state and various products. These experimental energies are compared with single point energies calculated at three different levels, B3LYP, B3P86, and MP2(full), using the 6-311+G(2d, 2p)) basis set with geometries and zero point energies calculated at the B3LYP/6-311G(d, p) level, as well as with additional calculations using basis sets that include core correlation on lithium. Good agreement between experiment and theory suggests that the reaction mechanisms have been reasonably elucidated and identifies the C3H4O2S deamination product as thiirane-carboxylic acid.