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We investigated the factors governing peptide backbone cleavages in electron capture dissociation (ECD) of some glycopeptides. ECD with infrared laser irradiation (activated ion ECD; AI ECD) and ECD with hot electron (<10 eV) irradiation (H ECD) were applied to two triantennary complex-type N-glycopeptides from bovine fetuin and their derivatives. The glycopeptides are those that did not show extensive backbone cleavage in conventional ECD [Hongo et al., J. Mass Spectrom. Soc. Jpn., 55, 77 (2007)]. Similar to the conventional ECD case, AI ECD on the glycopeptides only gave glycan fragmentation and radical losses. On the other hand, AI ECD on de-NeuNAc derivatives gave a mixed result; various c-type ions were generated from only one glycopeptide. H ECD on two deglycosylated peptides gave b-, y-, and a few w-type ions. The data indicated that the ECD backbone cleavage of these peptides was governed by multiple factors including the availability of the radical localizing site and the amount of protonation in the precursor ions.

Factors Governing Peptide Backbone Cleavages in Electron Capture Dissociation of Triantennary Complex-type N-Glycosylated Peptide