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Collision-induced dissociation has been used to study the fragmentations of two protonated diketopiperazines, protonated cyclic-glycylglycine and cyclic-alanylalanine. Protonated cyclo-AA lost CO and (CO + NH3) at low collision energies, channels attributed to dissociation of the O-protonated tautomer. Higher collision energies were required to dissociate protonated cyclo-GG, and the two lowest-energy products were the result of losses of one CO and two CO molecules. These occur from the higher-energy N-protonated tautomer, which is formed from the O-protonated tautomer by a 1,4-proton shift that has a high barrier (54.5 kcal mol(-1)) due to constraints imposed by the ring. Mechanistic schemes for four different dissociation channels, three from the N-protonated tautomer and one from the O-protonated tautomer, have been computed using density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. Comparison of the potential energy surfaces for the two protonated diketopiperazines reveals the factors behind this dichotomy of fragmentation pathways. The infrared multiple-photon dissociation spectrum of the [M+H-NH3-CO](+) ion (m/z 98) from protonated cyclo-M shows this product to be an oxazole, the lowest-energy isomer. (C) 2012 Elsevier B.V. All rights reserved.