Abstract Theoretical model calculations were performed to validate the ‘mobile proton’ model for protonated lysylglycine (KG). Detailed scans carried out at various quantum chemical levels of the potential energy surface (PES) of protonated KG resulted in a large number of minima belonging to various protonation sites and conformers. Transition structures corresponding to proton transfer reactions between different protonation sites were determined, to obtain some energetic and structural insight into the atomic details of these processes. The rate coefficients of the proton transfer reactions between the isomers were calculated using the Rice‐Ramsperger‐Kassel‐Marcus (RRKM) method in order to obtain a quantitative measure of the time‐scale of these processes. Our results clearly indicate that the added proton is less mobile for protonated KG than for peptides lacking a basic amino acid residue. However, the energy needed to reach the energetically less favorable but–from the point of view of backbone fragmentation–critical amide nitrogen protonation sites is available in tandem mass spectrometers operated under low‐energy collision conditions. Using the results of our scan of the PES of protonated KG, the dissociation pathways corresponding to the main fragmentation channels for protonated KG were also determined. Such pathways include loss of ammonia and formation of a protonated α‐amino‐ϵ‐caprolactam. The results of our theoretical modeling, which revealed all the atomic details of these processes, are in agreement with the available experimental results. Copyright © 2001 John Wiley & Sons, Ltd.