Scrambling of Sequence Information in Collision-Induced Dissociation of Peptides

Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
Journal of the American Chemical Society (Impact Factor: 12.11). 09/2006; 128(32):10364-5. DOI: 10.1021/ja062440h
Source: PubMed


Collision-induced dissociation (CID) of protonated YAGFL-NH2 leads to nondirect sequence fragment ions that cannot directly be derived from the primary peptide structure. Experimental and theoretical evidence indicate that primary fragmentation of the intact peptide leads to the linear YAGFLoxa b5 ion with a C-terminal oxazolone ring that is attacked by the N-terminal amino group to induce formation of a cyclic peptide b5 isomer. The latter can undergo various proton transfer reactions and opens up to form something other than the YAGFLoxa linear b5 isomer, leading to scrambling of sequence information in the CID of protonated YAGFL-NH2.

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    • "In recent years, Harrison and co-workers reported that middle-sized b n + (n≥4) ions undergo macrocyclization followed by ring-opening process in low-energy CID conditions [16] [17]. Numerous studies have provided a better understanding of the cyclization chemistry of b ions [18] [19] [20] [21] [22] [23] [24]. "
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    ABSTRACT: In 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 b2+ ions produced from the fragmentation of b6+ ions under low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). It should be noted that, among all other fragments, the b2+ and nominally b4+ (AAAA) ions ([M+H]+ → b6+ → b2+ (PX+) + b4+ (AAAA+) were mainly considered in this study. This is a unique example of consecutive cleavage of b6+ ions which fragments to b2+ and nominal b4+ ions. All structural and proton affinity calculations for b2+ 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-NH2 and PXAAAA-NH2 where X is phenylalanine (F), glutamic acid (E), tryptophan (W), and histidine (H) residue. Two main structural isomers of b2+ 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 b2+-PA, PF, and PE- ions are lower compared to the relative intensity of AAAA fragment ion. In contrast, b2+-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.
    Full-text · Article · Oct 2015 · International Journal of Mass Spectrometry
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    • "This can occur when amino acids undergo side chain fragmentation along with the usual peptide bond cleavages . Another phenomenon that can lead to misidentification is scrambling: [6] [15] upon collisional activation, the peptide may form a cyclic intermediate that re-opens leading to a permutation of the original sequence [16]. A review of fragmentation mechanisms of peptides was given by Paisz and Suhai [3]. "
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    ABSTRACT: In this work we have studied the collision induced dissociation (CID) of C-terminally amidated, protonated di- and tri-glycine by means of chemical dynamics simulations from on-the-fly electronic structure calculations using a semi-empirical Hamiltonian. The simulations represent a collision event between the peptide and an Ar-atom addressing the reactivity at "short" time-scales, i.e. up to 5 ps. Simulations were performed for different protonation sites, greatly influencing the reactivity in agreement with what is known from the "mobile proton" model of peptide dissociation. Results are then combined with ESI-MS/MS experiments to determine the fragmentation patterns. Additionally, we used IRMPD spectra to elucidate the structure of these peptides before collisional activation and the structures of some of the CID products. Results are also compared with threshold CID experiments reported in the literature for the non-amidated peptides. Chemical dynamics simulations can provide details on the fragmentation pathways observed. We also show that it is possible to identify the protonation state(s) that are populated in the different steps involved in the fragmentation process. Finally, the chemical dynamics approach is shown to be complementary to the more typical theoretical study of the potential energy surface that becomes more problematic (and sometimes impossible) for systems of increasing complexity.
    Full-text · Article · Aug 2015 · International Journal of Mass Spectrometry
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    • "[14] Recently, numerous experimental and theoretical studies have revealed that middle-sized b n (n = 5, 6, 7 …) ions undergo intramolecular head-to-tail cyclization to form a protonated cyclic peptide intermediate. [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] Upon proton transfer (PT), this cyclic structure subsequently reopens at different amide bonds to form a variety of C-terminal oxazolone b isomers with a permuted sequence, which may result in erroneous assignment of fragment ions for database searches. The lysine acetylation is one of the most prominent posttranslational modification found in proteins and plays vital roles in regulation of protein activity and gene expression. "
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    ABSTRACT: Characterization of ε-N-acetylated lysine containing peptides, one of the most prominent post-translational modifications of proteins, is an important goal for tandem mass spectrometry experiments. A systematic study for the fragmentation reactions of b ions derived from ε-N-acetyllysine containing model octapeptides (KAc YAGFLVG and YAKAc GFLVG) has been examined in detail. Collision-induced dissociation (CID) mass spectra of bn (n = 4-7) fragments of ε-N-acetylated lysine containing peptides are compared with those of N-terminal acetylated and doubly acetylated (both ε-N and N-terminal) peptides, as well as acetyl-free peptides. Both direct and nondirect fragments are observed for acetyl-free and singly acetylated (ε-N or N-terminal) peptides. In the case of ε-N-acetylated lysine containing peptides, however, specific fragment ions (m/z 309, 456, 569 and 668) are observed in CID mass spectra of bn (n = 4-7) ions. The CID mass spectra of these four ions are shown to be identical to those of selected protonated C-terminal amidated peptides. On this basis, a new type of rearrangement chemistry is proposed to account for the formation of these fragment ions, which are specific for ε-N-acetylated lysine containing peptides. Consistent with the observation of nondirect fragments, it is proposed that the b ions undergo head-to-tail macrocyclization followed by ring opening. The proposed reaction pathway assumes that bn (n = 4-7) of ε-N-acetylated lysine containing peptides has a tendency to place the KAc residue at the C-terminal position after macrocyclization/reopening mechanism. Then, following the loss of CO, it is proposed that the marker ions are the result of the loss of an acetyllysine imine as a neutral fragment. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.
    Full-text · Article · Dec 2014 · Journal of Mass Spectrometry
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