Detailed analysis of the possible fragmentation channels of protonated GGG suggests that a pre-dissociation cis-trans isomerization of the N-terminal amide bond has to take place when y1 ions are formed on the ‘diketopiperazine’ pathway. Quantum chemical calculations were performed in order to determine the effect of different isomerization states (trans-trans, cis-trans, trans-cis, and cis-cis) on the energetics of protonation of GGG at the most important protonation sites including the terminal amino group and amide oxygen and nitrogen atoms. These calculations indicate that cis-trans isomerization is energetically feasible for protonated GGG and the relative energy of the most stable such species that contain a cis amide bond is at a few kcal/mol calculated with respect to the trans-trans global minimum. Analysis of the possible pathways for the cis-trans isomerization suggests that this process involves species protonated at the nitrogen of the N-terminal amide bond. Detailed discussion of the fate of such species indicates that cis-trans isomerization of the N-terminal amide bond of protonated GGG is kinetically controlled while a low-energy pathway connecting the most stable trans-trans and cis-trans species no doubt exists. Copyright © 2001 John Wiley & Sons, Ltd.