Investigation of gas phase ion structure for proline-containing b 2 ion

Abstract. It is well-known that oxazolone b 2 ions fragment extensively by elimination of CO to form a 2 ions, which often fragment further to form a 1 ions. Less well-known is that some oxazolone b 2 ions may fragment directly to form a 1 ions. The present study uses energy-resolved collision-induced dissociation experiments to explore the occurrence of the direct b 2 →a 1 fragmentation reaction. The experimental results show that the direct b 2 →a 1 reaction is generally observed when Gly is the C-terminal residue of the oxazolone. When the C-terminal residue is more complex, it is able to provide increased stability of the a 2 product in the b 2 →a 2 fragmentation pathway. Our computational studies of the relative critical reaction energies for the b 2 →a 2 reaction compared with those for the b 2 →a 1 reaction provide support that the critical reaction energies are similar for the two pathways when the C-terminal residue of the oxazolone is Gly. By contrast, when the nitrogen of the oxazolone ring in the b 2 ion does not bear a hydrogen, as in the Ala-Sar and Tyr-Sar (Sar=N-methylglycine) oxazolone b 2 ions, a 1 ions are not formed but rather neutral imine elimination from the N-terminus of the b 2 ion becomes a dominant fragmentation reaction. The M06-2X/6-31+G(d,p) density functional theory calculations are in general agreement with the experimental data for both types of reaction. In contrast, the B3LYP/6-31+G(d,p) model systematically underestimates the barriers of these S N 2-like b 2 →a 1 reaction. The difference between the two methods of barrier calculation are highly significant (PG0.001) for the b 2 →a 1 reaction, but only marginally significant (P=0.05) for the b 2 →a 2 reaction. The computations provide further evidence of the limitations of the B3LYP functional when describing S N 2-like reactions.

Section: Mechanistic Considerationssupporting

confidence: 88%

Formation of a₁ Ions Directly from Oxazolone b₂ Ions: an Energy-Resolved and Computational Study

Bythell

Harrison

2015

“…missing because the radical ion does not contain leucine. The b 2 -H ion corresponds to abstraction of a hydrogen from the regular b 2 ion that is formed via a low-energy charge-directed dissociation channel [13,14,16,43,45,52]. These hydrogen-deficient b-type ions have been observed in previous radical ion fragmentation experiments [13,14,16,43,45].…”

Section: Radical-driven Fragmentation At Serine and Threoninementioning

confidence: 80%

Radical-driven dissociation of odd-electron peptide radical ions produced in 157 nm photodissociation

Zhang

Reilly

2009

Odd-electron a ϩ 1 radical ions generated in the 157 nm photodissociation of peptide ions were investigated in an ion trap mass spectrometer. To localize the radical, peptide backbone amide hydrogens were replaced with deuterium. When the resulting radical ions underwent hydrogen elimination, no H/D scrambling was obvious, suggesting that without collisional activation, the radical resides on the terminal ␣-carbon. Upon collisional excitation, oddelectron radical ions dissociate through two favored pathways: the production of a-type ions at aromatic amino acids via homolytic cleavage of backbone C ␣ -C(O) bonds and side-chain losses at nonaromatic amino acids. When aromatic residues are not present, nonaromatic residues can also lead to a-type ions. In addition to a-type ions, serine and threonine yield c n-1 and a n-1 ϩ 1 ions where n denotes the position of the serine or threonine. All of these fragments appear to be directed by the radical and they strongly depend on the amino acid side-chain structure. In addition, thermal fragments are also occasionally observed following cleavage of labile Xxx-Pro bonds and their formation appears to be kinetically competitive with radical migration. (J Am Soc Mass

“…In addition to chain length, it is highly likely that individual residues in the chain will influence the amide bond cleaved. In this respect, Wysocki and coworkers [23] have observed that doubly-protonated Val-Pro-AlaPro-Arg shows extensive cleavage at the N-terminal amide bond to form both y 4 and y 4 ϩ2 ions with only minor cleavage of the second amide bond. They also observed that doubly-protonated Val-Pro-Asp-Pro-Arg showed major cleavage C-terminal to the Asp residue to give the complementary b 3 and y 2 ions by charge separation.…”

Section: Discussionmentioning

confidence: 99%

Charge-separation reactions of doubly-protonated peptides: Effect of peptide chain length

Harrison

2009

The collision induced dissociation of doubly-protonated (Ala) x His (x ϭ 5, 6,7,8,10) peptides have been studied. The major fragmentation reactions observed are symmetrical amide bond cleavages to give the complementary b m and y N-m ions, where N is the total number of residues in the peptide. Minor asymmetric cleavage to give doubly-protonated y ions also is observed, involving cleavage near the N-terminus. The shorter peptides (x ϭ 5, 6, 7) show major cleavage of the second amide bond to yield b 2 and y N-2 ions, while (Ala) 10 His shows major symmetrical cleavage at the fourth and fifth amide bonds. T andem mass spectrometry has become a widely used method for deriving sequence information for peptides and proteins [1][2][3]. Protein identification in the field of proteomics most often involves protein digestion by trypsin, with identification and sequencing of the peptides produced by collision-induced dissociation of the singly-or multiply-protonated peptides resulting from soft ionization methods such as electrospray ionization [4]. Trypsin usually cleaves proteins C-terminal to arginine or lysine with the result that the peptides produced have a highly basic residue at the C-terminus. Such basic residues will localize a proton on the basic side chain [5], which often leads to fragmentation associated with the basic site rather than cleavage along the peptide backbone that is necessary for peptide sequencing. As a consequence fragmentation of doubly-or multiply-charged peptides in which there is a mobile proton [5] has been found to provide more complete sequence information.There have been many detailed studies of the dissociation chemistry of singly-protonated nontryptic peptides; these studies have been summarized in a recent review [6]. On the other hand, despite the importance of the fragmentation chemistry of doubly-protonated tryptic peptides in proteomics, much less is known in detail concerning the fragmentation reactions of such species. A common fragmentation reaction of doublyprotonated peptides is charge separation in which amide bond cleavage leads to complementary singlycharged b and y ions [7][8][9][10]. Recently, Zubarev and coworkers [11] have carried out a statistical analysis of a large database of CID spectra of doubly-protonated tryptic peptides. They found that the charge separation spectra fell into two well separated statistical classes. Class I CID spectra were dominated by the y N-2 ion signal (and, presumably, the corresponding b 2 ion) where N is the number of amino acid residues in the peptide. By contrast, Class II CID spectra showed other y ions as the most abundant charge-separation products. There is some evidence from their analysis that cleavage of the second amide bond to form y N-2 is particularly important for smaller peptides and decreases in relative importance with increasing size of the peptide. It appeared of interest to study a series of peptides where the only variable is the number of residues in the peptide so that the effect of chain length can be separated...