The relative charge ratio between C and N atoms in amide bond acts as a key factor to determine peptide fragment efficiency in different charge states

Abstract

The influence of charge state on the peptide dissociation behavior in tandem mass spectrometry (MS/MS) is worthy of discussion. Comparative studies of singly- and doubly-protonated peptide molecules are performed to explore the effect and mechanism of charge state on peptide fragmentation. In view of the charge-directed cleavage of protonated peptides described in the mobile proton model, radiolytic oxidation was applied to change the charge distribution of peptides but retain the sequence. Experimental studies of collision energy-dependent fragmentation efficiencies coupled with quantum chemical calculations indicated that the cleavage of ARRA and its side-chain oxidation products with oxygen atoms added followed a trend that doubly-protonated peptides fragment more easily than singly-protonated forms, while the oxidation product with the guanidine group deleted showed the opposite trend. By analyzing the charge distribution around the amide bonds, we found that the relative charge ratios between C and N atoms (Q(C)/Q(N)) in the amide bonds provided a reasonable explanation for peptide fragmentation efficiencies. An increase of the Q(C)/Q(N) value of the amide bond means that a peptide fragments more easily, and vice versa. The results described in this paper provide an experimental and calculation strategy for predicting peptide fragmentation efficiency.

Structural characterization of Momordica charantia L. (Cucurbitaceae) oligopeptides and the detection of their capability in non-small cell lung cancer A549 cells: induction of apoptosis

“…The peptides are usually protonated under ESI-MS/MS conditions, and fragmentations mostly occur at the amide bonds because it is difficult to break the chemical bonds of the side chains at such low energy. 18 Therefore, the b and y ions are the main fragment ions when the collision energy is <200 eV. MCLO-12 was analyzed by HPLC-ESI-MS for molecular mass determination and peptide characterization.…”

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

“…In the work presented here, model peptide Phe‐Met‐Arg‐Phe (FMRF) with a Met residue (quite susceptible to oxidation) was subjected to H 2 O 2 oxidation. Side‐chain oxidation on peptide FMRF would change its charge distribution25 and simultaneously resolve the inconsistent amide bond sequence/protonation sites of previous studies13–14. The MS/MS data (fragmentation energy curves and fractional abundances of fragment ions) of the native and oxidized peptides and their charge distributions obtained by quantum chemical calculations were incorporated to study the influence of oxidation on the charge distribution and the discrepant fragmentation of the native and oxidized FMRF.…”