We have studied multiple ionization and dissociation of a trapped protonated peptide (leucine enkephalin) as induced by keV singly and doubly charged ions (H(+), He(+, 2+)) to demonstrate the potential of keV ions as a future tool for peptide identification. In contrast to conventional excitation techniques, the fragmentation pattern exhibits very strong peaks due to loss of sidechains in addition to those due to backbone scission. The results can be understood on the basis of the energy deposited into the peptide via electronic stopping. A pronounced dependence of the fragmentation pattern on the electronic structure of the projectile ions can be attributed to different electron capture efficiencies from localized molecular orbitals.