Proposed nomenclature for peptide ion fragmentation

Chu, Ivan K.; Siu, Chi‐Kit; Lau, Justin Kai-Chi; Tang, Wai Kit; Mu, Xiaoyan; Lai, Cheuk-Kuen; Guo, Xinhua; Xian, Wang; Li, Ning; Xia, Yu; Kong, Xianglei; Oh, Han Bin; Ryzhov, Victor; Tureček, František; Hopkinson, Alan C.; Siu, Kin Wai Michael

doi:10.1016/j.ijms.2015.07.021

Cited by 70 publications

(48 citation statements)

References 30 publications

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“…The backbone CO-NH bond and side-chain dissociations follow a similar trend as observed for the analogous Arg-C- The all-inclusive fragment ion nomenclature is used [32]. Conversion to the Roepstorff-Fohlman-Biemann system [35,36] is as follows:…”

Section: Resultsmentioning

confidence: 96%

“…This feature and the ion charge and electron parity are conveniently expressed by the all-inclusive nomenclature described recently that uses the hydrogen count in neutral peptide fragments as reference [32]. The conversion to the common Roepstorff-Fohlman-Biemann nomenclature [35,36] is as follows for the fragment ions described here:…”

Section: Note On Nomenclaturementioning

confidence: 99%

“…The electron transitions leading to the second (B) doublet excited state (ΔE exc = 3.509 eV, 353 nm, oscillator strength f = 0.024) are shown for [ • AAAR + ] (Figure 4). These transitions lead to absorption at 355 nm and photodissociation; note, however, that the absorption maximum is The all-inclusive fragment ion nomenclature is used [32]. Conversion to the Roepstorff-Fohlman-Biemann system [35,36] (Table 1).…”

Section: [Z 4 + H] +• Ionsmentioning

confidence: 99%

“…We selected to study UVPD of the following types of z-ions. The first type is [ • AXAB + ], or [z 4 + H] +• , ions (for nomenclature see Ref [32]), that have the C α -radical defect at the deaminated N-terminal Ala residue and contain a common chromophore for all combinations of X and B. Second, ETD fragment ions by loss of ammonia from peptides of the Lys-C-terminated (AAXAK) series were studied.…”

Section: Introductionmentioning

confidence: 99%

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Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

Nguyen

Tureček

2017

J. Am. Soc. Mass Spectrom.

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, where X = A, C, D, E, F, G, H, K, L, M, N, P, Y, and W, were generated by electron transfer dissociation of peptide dications and investigated by MS 3 -nearultraviolet photodissociation (UVPD) at 355 nm. Laser-pulse dependence measurements indicated that the ion populations were homogeneous for most X residues except phenylalanine. UVPD resulted in dissociations of backbone CO─NH bonds that were accompanied by hydrogen atom transfer, producing fragment ions of the [y n ] + type. Compared with collision-induced dissociation, UVPD yielded less sidechain dissociations even for residues that are sensitive to radical-induced side-chain bond cleavages. The backbone dissociations are triggered by transitions to second (B) excited electronic states in the peptide ion R-CH • -CONH-chromophores that are resonant with the 355-nm photon energy. Electron promotion increases the polarity of the B excited states, R-CH + -C • (O -)NH-, and steers the reaction to proceed by transfer of protons from proximate acidic C α and amide nitrogen positions.

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Section: Resultsmentioning

confidence: 96%

Section: Note On Nomenclaturementioning

confidence: 99%

Section: [Z 4 + H] +• Ionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

Nguyen

Tureček

2017

J. Am. Soc. Mass Spectrom.

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“…To describe in a uniform way the fragment ions originating from different types of peptide cation-radicals, we adopt the allinclusive nomenclature system introduced recently [40]. Briefly, this uses the original Biemann system of naming peptide fragments according to the backbone bond being broken [20], but explicitly assigning the charge, radical, and number of hydrogen atoms included in the fragment ion [40].…”

Section: Note On Nomenclaturementioning

confidence: 99%

Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

Viglino

Lai

et al. 2016

J. Am. Soc. Mass Spectrom.

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Abstract. We report a comprehensive study of collision-induced dissociation (CID) and near-UV photodissociation (UVPD) of a series of tyrosine-containing peptide cation radicals of the hydrogen-rich and hydrogen-deficient types. Stable, long-lived, hydrogen-rich peptide cation radicals, such as [AAAYR + 2H] +• and several of its sequence and homology variants, were generated by electron transfer dissociation (ETD) of peptide-crown-ether complexes, and their CID-MS 3 dissociations were found to be dramatically different from those upon ETD of the respective peptide dications. All of the hydrogen-rich peptide cation radicals contained major (77%-94%) fractions of species having radical chromophores created by ETD that underwent photodissociation at 355 nm. Analysis of the CID and UVPD spectra pointed to arginine guanidinium radicals as the major components of the hydrogen-rich peptide cation radical population. Hydrogen-deficient peptide cation radicals were generated by intramolecular electron transfer in Cu II (2,2′:6′,2″-terpyridine) complexes and shown to contain chromophores absorbing at 355 nm and undergoing photodissociation. The CID and UVPD spectra showed major differences in fragmentation for [AAAYR] +• that diminished as the Tyr residue was moved along the peptide chain. UVPD was found to be superior to CID in localizing C α -radical positions in peptide cation radical intermediates.

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Evidence for the Prerequisite Formation of Phenoxyl Radicals in Radical‐Mediated Peptide Tyrosine Nitration In Vacuo

Lai

Tang

Siu

et al. 2019

Chemistry A European J

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The elementary mechanism of radical‐mediated peptide tyrosine nitration, which is a hallmark of post‐translational modification of proteins under nitrative stress in vivo, has been elucidated in detail by using an integrated approach that combines the gas‐phase synthesis of prototypical molecular tyrosine‐containing peptide radical cations, ion–molecule reactions, and isotopic labeling experiments with DFT calculations. This reaction first involves the radical recombination of .NO2 towards the prerequisite phenoxyl radical tautomer of a tyrosine residue, followed by proton rearrangements, finally yielding the stable and regioselective 3‐nitrotyrosyl residue product. In contrast, nitration with the π‐phenolic radical cation tautomer is inefficient. This first direct experimental evidence for the elementary steps of the radical‐mediated tyrosine nitration mechanism in the gas phase provides a fundamental insight into the regioselectivity of biological tyrosine ortho‐nitration.

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Proposed nomenclature for peptide ion fragmentation

Cited by 70 publications

References 30 publications

Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

Near-UV Photodissociation of Tryptic Peptide Cation Radicals. Scope and Effects of Amino Acid Residues and Radical Sites

Ground and Excited-Electronic-State Dissociations of Hydrogen-Rich and Hydrogen-Deficient Tyrosine Peptide Cation Radicals

Evidence for the Prerequisite Formation of Phenoxyl Radicals in Radical‐Mediated Peptide Tyrosine Nitration In Vacuo

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