[ M·GlyGlyHis]+ ( M = Li, Na, K, Rb, Cs, and Ag) complexes were generated using the electrospray ionization method and were subjected to collision-induced dissociation. Metal ion loss is the primary dissociation channel for [Cs·GlyGlyHis]+ whereas other complexes yield metal-bound peptide sequence ions and dehydrated ions as the main products. [Li·GlyGlyHis]+ and [Ag·GlyGlyHis]+ also generate product ions that are not observed for other complexes. Density functional theory calculations suggest that metal ion–peptide ligand interaction occurs through covalent interactions in [Li·GlyGlyHis]+ and [Ag·GlyGlyHis]+, and through electrostatic attraction in [Na·GlyGlyHis]+, [K·GlyGlyHis]+, [Rb·GlyGlyHis]+, and [Cs·GlyGlyHis]+. The calculations also suggest that fragmentation behavior of these complexes is affected by charge transfer to the ligand and ion-ligand interaction energy, and to a lesser extent by the ion size.