Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides with Three or More Charges

A kinetic model, based on the “mobile proton” model of peptide fragmentation, has been reported previously for quantitative prediction of low-energy collision-induced dissociation (CID) spectra of singly or doubly charged peptides. For peptides with three or more charges, however, the simulation process is complex and time-consuming. This paper describes a simplified model for quantitative prediction of CID spectra of peptide ions with three or more charges. Improvements on other aspects of the model were also made to accommodate large peptides. The performance of the simplified model was evaluated by generating predictions for many known highly charged peptides that were not included in the training data set. It was shown that the model is able to predict peptide CID spectra with reasonable accuracy in fragment ion intensities for highly charged peptide ions up to 5000 u in mass.