Abstract:
The fragmentation characteristics of protonated peptides have been investigated using
tandem mass spectrometry (MS/MS) under various fragmentation regimes and detailed
density functional theory (DFT) reaction pathway calculations. The DFT calculations
predict novel salt-bridge stabilized transition structures as well as consecutive reactions
occurring in proton-bound dimers for some of the ions detected in the MS/MS
experiments. Four previously unknown protonated peptide fragmentation mechanisms are
described in this thesis based on the theoretical and experimental results. These results
have been evaluated using the mobile proton model and the more recently introduced
pathways in competition (PIC) protonated peptide fragmentation model. The mobile
proton model cannot adequately explain these experimental findings. The PIC model on
the other hand, considers post-cleavage as well as pre-cleavage and bond-cleavage
events, which enable these complicated protonated peptide fragmentation pathways to be
rationalized.
