Prediction of electron-transfer/capture dissociation spectra of peptides.

An empirical model, based on classic kinetics, was developed for quantitative prediction of electron-transfer dissociation (ETD) and electron-capture dissociation (ECD) spectra of peptides. The model includes most fragmentation pathways described in the literature plus some additional pathways based on the author's assumptions and observations. The ETD model was trained with more than 7000 ETD spectra, with and without supplemental activation. The ECD model was trained with more than 6000 ECD spectra. The trained ETD and ECD models are able to predict ETD and ECD spectra with reasonable accuracy in ion intensities for peptide precursors up to 4000 u in mass.