Histidine, lysine, and arginine radical cations have been generated through collision-induced dissociation (CID) of complexes [Cu-II(auxiliary ligand)(n)(amino acid)](center dot 2+), using tri-, bi-, as well as monodentate auxiliary ligands. On the basis of the observed CID products, the existence of two isomeric amino-acid populations is postulated. The Type 1 radical cations of histidine and lysine, stable on the mass spectrometer time scale, were found to lose water, followed by the loss of carbon monoxide under more energetic CID conditions. The arginine Type 1 radical cation behaved differently, losing dehydroalanine. The Type 2 radical cations were metastable and easily fragmented by the loss of carbon dioxide, effectively preventing direct observation. Type 1 radical cations are proposed to result from neutral (canonical) amino-acid coordination, whereas Type 2 radical cations are from zwitterionic amino-acid coordination to copper in the complex. The ratio of Type 1/Type 2 ions was found to be dependent on the auxiliary ligand, providing a method of controlling which radical cation would be formed primarily. Density functional calculations at B3LYP/6-311++G(d,p) have been used to determine the relative energies of five His(center dot+) isomers. Barriers against interconversion between the isomers and against fragmentation have been calculated, giving insight as to why the Type 1 ions are stable, while only fragmentation products of the Type 2 ions are observable under CID conditions.