title: The charge ratio between O and N on amide bonds: a new approach to the mobile proton model.
abstract: The influence of charge distribution on the cleavage of the peptides was investigated by fragmentation efficiency curves and quantum chemical calculations in order to clarify the fragmentation mechanism in this paper. The peptide Arg-Gly-Asp-Cys (RGDC) was oxidized to change the charge distribution, but its main sequence was retained. Under this study, it was illustrated that the fragmentation of the peptide RGDC became easier with each addition of an O atom to the Cys hydrosulfide group and the relative charge ratios between O and N (QO/QN) in the amide bonds had much to do with the cleavage of the peptide RGDC. For each amide bond, the situations coincided with overall conclusion: the increase of the QO/QN values results in a higher fragmentation efficiency and vice versa. The methods which combined fragmentation efficiency curves with the charge distribution of peptides provided a way to refine the mobile proton model for peptide fragmentation and to probe the discrepant fragmentation of peptides in peptide/protein identification.
authors.affiliation: Shandong Key Laboratory of Water Pollution Control and Resource 4 Reuse, School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, Shandong Province, 27# Shanda South Road, Jinan 250100, PR China.
authors.forename: Meijie
authors.initials: M
authors.lastname: Wang
authors.forename: Pengjun
authors.initials: P
authors.lastname: Zhang
authors.forename: Wansong
authors.initials: W
authors.lastname: Zong
authors.forename: Qifei
authors.initials: Q
authors.lastname: Xu
authors.forename: Rutao
authors.initials: R
authors.lastname: Liu
mesh_terms: D000577:Amides / Q000737:chemistry*; D003545:Cysteine / Q000737:chemistry; D008956:Models, Chemical; D009584:Nitrogen / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry*; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry*; D011522:Protons; D011789:Quantum Theory; D053719:Tandem Mass Spectrometry
chemical_list: D000577:Amides; D009842:Oligopeptides; D010446:Peptide Fragments; D011522:Protons; C568214:arginyl-glycyl-aspartyl-cysteine; C047981:arginyl-glycyl-aspartic acid; D003545:Cysteine; D009584:Nitrogen; D010100:Oxygen