Clusters of singly deprotonated tripeptide PheGlyGly bound to doubly charged alkaline earth, transition, and lanthanide metal ions are generated and analyzed through electrospray ionization/collision-induced dissociation mass spectrometry (CID MS/MS). Experimental results show that these clusters undergo fragmentation to generate metal-bound ion products. The extent of fragmentation for [Ca·PheGlyGly-H]+, [Sr·PheGlyGly-H]+, and [Ba·PheGlyGly-H]+ shows metal ion radius dependence, whereas no such correlation is found for [Cu·PheGlyGly-H]+, [Zn·PheGlyGly-H]+, [Fe·PheGlyGly-H]+, and [Mn·PheGlyGly-H]+. Fragmentation behavior of [Eu·PheGlyGly-H]+ is similar to those of both the alkaline earth and transition metal-bound clusters, with stronger characteristics of the former. Density functional theory calculations are performed to assign structures and make qualitative comparisons of ion–ligand binding energies for the cluster series. The binding energy is greater for transition metal ion-bound species than the alkaline earth metal ion-bound ones due to ligand–field stabilization, and Cu2+ adopts a weakly negative charge upon complexation, leading to unique dissociation behavior of [Cu·PheGlyGly-H]+. Observation of sequence ions and those arising from dehydration and deammoniation supports the mobile cation model, and consideration of the dissociation energetics suggests the possibility that the cluster fragmentation process may involve predissociation.