The metastable ion fragmentation reactions of protonated a-amino acids were recorded. In addition, the lowenergy collision-induced dissociation (CID) reactions were studied as a function of collision energy and breakdown graphs, expressing the energy dependence of the fragmentation reactions, were established for a variety of protonated amino acids. The fragmentation reactions observed depend strongly on the identity of the R group in H,NCH(R)COOH. Protonated amino acids containing only alkyl groups in the side-chain fragment primarily by elimination of (H,O + CO) in both metastable and CID reactions. Hydroxylic and acidic amino acids show loss of H,O and loss of (H,O + CO) from MH' with the H,O loss occurring from the side-chain and (H,O + CO) loss occurring from the acarbohydroxy group. Amidic amino acids show NH, loss from the side-chain and (H,O + CO) loss from the carbohydroxy group. Aromatic and sulfur-containing amino acids show loss of NH, from MH', as does lysine. Protonated arginine shows a variety of fragmentation pathways, including elimination of NH, , elimination of neutral gnanidine and formation of protonated guanidine. The energy-dependent breakdown graphs elucidate a variety of secondary fragmentation reactions of the primary fragment ions.