Mechanism of fragmentation reactions of [MH]+ ions obtained from peptides by liquid secondary ion mass spectrometry

‘Soft ionization’ spectra upon particle bombardment of peptides usually show abundant [MH]+ ions. They correspond to different types of [MH]+ ions, since proton addition is possible at different sites of the molecule. Fragmentation reactions are triggered by the site of charge localization. The proton in a free peptide is located mainly at the basic nitrogen. Therefore, in many cases, immonium fragments of the N-terminal amino acid are produced. By contrast, in an acylated peptide, all nitrogens have about the same basicity. [MH]+ ions are produced in which the charge must be located at an amide nitrogen, resulting in a preferential cleavage of the peptide bond by producing an amine and an acylium ion, which often decomposes by loss of CO. Therefore, in acylated peptides, the tendency to produce structurally specific fragments is considerably higher than in free peptides.