Gas-phase structures and proton affinities of N-terminal proline containing b2+ ions from protonated model peptides

Abstract

a b s t r a c tIn this study, we investigated the effect of the second amino acid identity of hexapeptides on gas-phase structures and the proton affinities of N-terminal proline containing b 2 + ions produced from the fragmentation of b 6 + ions under low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). It should be noted that, among all other fragments, the b 2 + and nominallywere mainly considered in this study. This is a unique example of consecutive cleavage of b 6 + ions which fragments to b 2 + and nominal b 4 + ions. All structural and proton affinity calculations for b 2 + ions were carried out with the B3LYP/6-31+G(d,p) level of theory. The study utilized C-terminal amidated model peptides consisting of PAAAAA-NH 2 and PXAAAA-NH 2 where X is phenylalanine (F), glutamic acid (E), tryptophan (W), and histidine (H) residue. Two main structural isomers of b 2 + ions, namely oxazolone and diketopiperazine, have been considered for the computations. The results demonstrated that the proton affinities of oxazolone isomers of PX are greater than its diketopiperazine isomers. Higher correlation coefficient is calculated if the structure of PX is considered as oxazolone rather than diketopiperazine isomer. Additionally, a linear fit is observed between intensity ratio (PX/AAAA) and calculated proton affinities of PX ions. Additionally, MS/MS results revealed that the relative intensities of b 2 + -PA, PF, and PE-ions are lower compared to the relative intensity of AAAA fragment ion. In contrast, b 2 + -PW and PH-ions have higher relative intensities compared to the AAAA ion. This behavior is explained by the proton affinities of fragment ions computationally.

Energetic switch of the proline effect in collision‐induced dissociation of singly and doubly protonated peptide Ala‐Ala‐Arg‐Pro‐Ala‐Ala

“…When the Arg residue locates adjacent to the N‐terminal of Pro as in [AARPAA+H] + , both and ions were observed (Figure B). This phenomenon looks straight forward because the N‐terminal fragment AAR can win the proton in the competition with the C‐terminal fragment PAA due to the high proton affinity of Arg . However, although the CID breakdown graph shows that the backbone cleavage still mainly occurred at the amide bond N‐terminal to Pro, the total abundance of (Figure B′) is much lower compared with the amount of in the CID spectra of [AAAPAA+H] + .…”

“…This phenomenon looks straight forward because the N-terminal fragment AAR can win the proton in the competition with the C-terminal fragment PAA due to the high proton affinity of Arg. 21,[26][27][28][29] However, although the CID breakdown graph shows that the backbone cleavage still mainly occurred at the amide bond N-terminal to Pro, the total abundance of b þ 3 þ y þ 3 ( Figure 2B′) is much lower compared with the amount of y þ 3 in the CID spectra of [AAAPAA+H] + . Figure 3 shows the relative bond-cleavage ratio of different amide bonds.…”

Spectroscopic Evidence for Lactam Formation in Terminal Ornithine b2+ and b3+ Fragment Ions

“…Structural identification of peptides and their fragments is a focus of proteomics-related mass spectrometry research. Due to their ubiquity in collision-induced dissociation (CID) and infrared multiple photon dissociation (IRMPD) pathways, the formation, and structure of btype ions are of particular interest to these studies [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21]. Until now, two major pathways have been documented for the smallest multiple-residue b-ion system, b 2…”