QCMS as a new method for providing insight into peptide fragmentation: The influence of the side-chain and inter-side-chain interactions.

The identification of peptides and proteins from tandem mass spectra is a difficult task and multiple tools have been developed to aid this identification. We present a new method called quantum chemical mass spectrometry for materials science (QCMS ), which is based on quantum chemical calculations of bond orders, reaction, and transition-state energies at the DFT/B3LYP/6-311+G* level of theory. The method was used to describe the fragmentation pathways of five X-His-Ser tripeptides with X = Asn, Asp, Glu, Ser, and Trp, thereby focusing on the influence of the side chain and inter-side-chain interactions on the fragmentation.