The dominant fragmentation processes in the gas phase of the doubly-charged complexes formed by the association of Ca2+ to cysteine, namely the loss of ammonia and the formation of ammonium ion, have been analyzed in detail in terms of the reaction force profiles, the chemical potential and the reaction electronic flux (REF) calculated at the B3LYP/6-311+G(d,p) level of theory. These analyses show that the investigated ammonia-loss processes can be classified as elementary reactions, whereas the Coulomb explosions yielding NH4+ + [CaC3H3O2S](+) include, at least two elementary steps. The variations of the chemical potential and in particular of the REF permits to identify very easily the subtle differences that exist between processes, such as the ammonia-loss ones which are apparently equal. The bond breaking and the bond formation processes can be followed through the evolution of the corresponding internuclear distances along the reaction coordinate; but the most precise information on where the bond formation or the bond fissions are complete is readily obtained by examining the derivatives of the corresponding bond orders along the reaction coordinate.