Quantum chemical and RRKM calculations were performed on protonated GGG in order to determine the atomic details of the main fragmentation pathways leading to formation of b2,y1, and y2 ions. Formation of y1 ions on the ‘diketopiperazine’ pathway is initiated from relatively high-energy C-terminal amide nitrogen protonated species for which the N-terminal amide bond is in the cis isomerization state. The reaction goes through a transition structure which is only slightly less favored than the reactive configuration itself. RRKM calculations indicate that this reaction is extremely fast as soon as the fragmenting species have more internal energy than the reaction threshold. The calculated energetics suggests that y1 ions are formed on the ‘diketopiperazine’ pathway with a non-negligible (6–10 kcal/mol) reverse activation barrier. Investigation of species occurring during the formation of b2 ions having an oxazolone structure indicates that y1 ions can be formed also from intermediates previously thought to result in only b2 ions. As the first step of the ‘bx-yz’ pathway proposed here the extra proton must reach the nitrogen of the C-terminal amide bond. Attack of the N-terminal amide oxygen on the carbon center of the C-terminal amide bond results in formation of the oxazolone ring while the detaching G leaves the precursor ion. Under low-energy collision conditions the complex of protonated 2-aminomethyl-5-oxazolone and G can rearrange to form a proton-bonded dimer of these species. In such circumstances the extra proton is shared by the two monomers and dissociation of the dimer will be determined by the thermochemistry involved. Based on the ‘bx-yz’ pathway one can easily explain the linear relationship between the logarithm of the y1/b2 ion abundance ratio and the proton affinity of the C-terminal amino acid substituent for the series of H-Gly-Gly-Xxx-OH tripeptides where Xxx was varied (Morgan DG, Bursey MM. Org. Mass. Spectrom. 1994; 29: 354). The calculated energetics indicates that both y1 and b2 ions are formed with no reverse activation barrier on the ‘bx-yz’ pathway. Copyright © 2002 John Wiley & Sons, Ltd.