Influence of charge distribution on the discrepant MS/MS fragmentation of the native and oxidized FMRF: evidence for the mobile proton model

Abstract

Using the mobile proton model as a framework, the influence of charge distribution on the discrepant fragmentation of peptides FMRF, FM(O)RF and FM(O(2))RF (with united peptide sequence) was explored by mass spectrometry experiments and quantum chemical calculations. With the added O atoms, more negative charges were prompted to deposit in the main protonation sites of the oxidation products. Consequently, the solvated proton to the oxidized peptides could flow to the amide bonds in an easier manner and made these bonds fragment easily. Oxidation also induced the discrepant fragmentation of these bonds in a predictable manner: the more negative charges deposited in an amide bond, the more daughter ions (a(n), b(n), y(n) ions and their derivatives) were produced. The combined methods proposed here refined the mobile proton model for peptide fragmentation and opened the way to probe the discrepant fragmentation of peptides in peptide/protein identification.

Comparative Studies on the Discrepant Fragmentation Mechanisms of the Gly-Asp-Gly-Arg and Arg-Gly-Asp-Gly: Evidence for the Mobile Proton Model

“…22 Previous studies testified that conformations could be searched and determined effectively at this level. 23,24 Calculations of electronic and structural properties allowed direct comparisons with the experimental measurements, including the analysis of charge distributions. Based on the optimized structures of GDGR and RGDG, the ionizing proton was mobilized from the N1 site to N2, N3, N4, and N5 positions (numbers shown in Scheme 2) separately to simulate the movement of the proton in the mobile proton model.…”