In a hybrid instrument under minimal multiple-collision conditions, the collision-induced fragmentation of the [M + H]+ ions of tetraalanine and tetraglycine are dominated by the gamma 2 fragment, in distinction to the fragmentation of the [M + H]+ ions of hexa- and octaalanine and -glycine; these latter fragmentations are instead a distribution of b and y ions, and to a lesser extent a ions. This difference may be rationalized on the basis of control of the fragmentation by the most basic site in the peptide, which may be identified by taking internal hydrogen bonding into account. On increasing the collision energy from 10 to 150 eV, a, b and y ions of lower mass appear; and in several cases a peak due to a smaller b ion becomes the base peak. The ion distribution in the spectra of these protonated peptides serves as a baseline from which the effects of conformation on side-group rearrangements and other fragmentations may be explored.