Abstract Pathways for proton transfer in the histidylglycine cation are examined in the gas‐phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero‐point energy are included, it is found that all the lowest energy barriers for proton transfer between the N‐terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring. In mass spectrometric techniques employing collision‐induced dissociation to dissociate protein complex ions or to fragment peptides, these barriers can be overcome, and the protons mobilized. Copyright © 2008 John Wiley & Sons, Ltd.