Prediction of dominant channels in collisional fragmentation of protonated short peptides

Abstract

Collisional fragmentation of protonated short peptides taking place in a linear quadrupole trap of a mass spectrometer is considered. A model of the fragmentation process is proposed which accounts for the collisional heating of the peptides due to the presence of a buffer inert gas. Dominant fragmentation channels for given temperature, pressure, excitation time and other parameters are predicted based on density functional calculations of the fragmentation pathways. The presented framework may be used for improving statistical significance assignments in mass spectrometry-based peptide/protein identification techniques.