Journal
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
Volume 388, Issue -, Pages 40-52Publisher
ELSEVIER
DOI: 10.1016/j.ijms.2015.07.025
Keywords
Collision induced dissociation; QM plus MM chemical dynamics; IRMPD; Peptides; Fragmentation mechanisms; Mass spectrometry
Funding
- UEVE
- KNUE
- NWO Chemical Sciences under VICI project [724.011.002]
- NWO
- National Research Foundation of Korea (NRF) [2015-0080]
- ANR DynBioReact [ANR-14-CE06-0029-01]
- National Research Foundation of Korea [2011-0008992] Funding Source: Korea Institute of Science & Technology Information (KISTI), National Science & Technology Information Service (NTIS)
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In this work we have studied the collision induced dissociation (CID) of C-terminally amidated, protonated di- and tri-glycine by means of chemical dynamics simulations from on-the-fly electronic structure calculations using a semi-empirical Hamiltonian. The simulations represent a collision event between the peptide and an Ar-atom addressing the reactivity at short time-scales, i.e. up to 5 ps. Simulations were performed for different protonation sites, greatly influencing the reactivity in agreement with what Is known from the mobile proton model of peptide dissociation. Results are then combined with ESI-MS/MS experiments to determine the fragmentation patterns. Additionally, we used IRMPD spectra to elucidate the structure of these peptides before collisional activation and the structures of some of the CID products. Results are also compared with threshold CID experiments reported in the literature for the non-amidated peptides. Chemical dynamics simulations can provide details on the fragmentation pathways observed. We also show that it is possible to identify the protonation state(s) that are populated in the different steps involved in the fragmentation process. Finally, the chemical dynamics approach is shown to be complementary to the more typical theoretical study of the potential energy surface that becomes more problematic (and sometimes impossible) for systems of increasing complexity. (C) 2015 Elsevier B.V. All rights reserved.
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