Bromine isotopic signature facilitates <i>de novo</i> sequencing of peptides in free‐radical‐initiated peptide sequencing (FRIPS) mass spectrometry

Nam, Jungjoo; Kwon, Hyuksu; Jang, Inae; Jeon, Aeran; Moon, Jingyu; Lee, Sun Young; Kang, Dukjin; Han, Sang Yun; Moon, Bongjin; Oh, Han Bin

doi:10.1002/jms.3539

Cited by 9 publications

(4 citation statements)

References 77 publications

(210 reference statements)

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“…Hydrogen‐deficient peptide radical cations can also be produced; for example, through photo‐dissociation of protonated peptides derivatized with photo‐labile covalent bonds, under ultraviolet (UV) or vacuum ultraviolet (VUV) irradiation . Peptide dissociation behavior in tert ‐butyl peroxycarbamate–, Vazo 68–, and TEMPO– (2,2,6,6‐tetramethylpiperidine‐1‐oxyl) based FRIPS (free radical–initiated peptide sequencing) MS has been analyzed in both positive‐ and negative‐ion modes for a number of peptides. The radical ion chemistry of a suite of S ‐ and N ‐nitrosopeptides has been investigated .…”

Section: Common Techniques For Formation Of Peptide Radical Ions In Tmentioning

confidence: 99%

Tautomerization and Dissociation of Molecular Peptide Radical Cations

Mu¹,

Song²,

Siu

et al. 2017

The Chemical Record

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Radical-mediated dissociations of peptide radical cations have intriguing unimolecular gas phase chemistry, with cleavages of almost every bond of the peptide backbone and amino acid side chains in a competitive and apparently "stochastic" manner. Challenges of unraveling mechanistic details are related to complex tautomerizations prior to dissociations. Recent conjunctions of experimental and theoretical investigations have revealed the existence of non-interconvertible isobaric tautomers with a variety of radical-site-specific initial structures, generated from dissociative electron transfer of ternary metal-ligand-peptide complexes. Their reactivity is influenced by the tautomerization barriers, perturbing the nature, location, or number of radical and charge site(s), which also determine the energetics and dynamics of the subsequent radical-mediated dissociatons. The competitive radical- and charge-induced dissociations are extremely dependent on charge density. Charge sequesting can reduce the charge densities on the peptide backbone and hence enhance the flexibility of structural rearrangement. Analysing the structures of precursors, intermediates and products has led to the discovery of many novel radical migration prior to peptide backbone and/or side chain fragmentations. Upon these successes, scientists will be able to build peptide cationic analogues/tautomers having a variety of well-defined radical sites.

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Section: Common Techniques For Formation Of Peptide Radical Ions In Tmentioning

confidence: 99%

Tautomerization and Dissociation of Molecular Peptide Radical Cations

Mu¹,

Song²,

Siu

et al. 2017

The Chemical Record

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“…In this study, we report a new approach to characterize the protein structure in the gas phase using TEMPO ((2,2,6,6-tetramethylpiperidine-1-yl)-oxyl)-assisted free-radical-initiated peptide sequencing (FRIPS) MS (see Scheme ). − The TEMPO-assisted FRIPS MS is a radical-based fragmentation technique, in which the radical precursor (i.e., TEMPO–Bz–CO− ) is conjugated to the N-terminus of a peptide ( TEMPO–Bz–CO–NH–peptide ). When thermal activation is given to the peptide precursor, a free radical is generated through homolytic bond cleavage between the benzylic carbon and the oxygen of the TEMPO moiety, leading to the formation of •Bz–CO–NH–peptide.…”

Section: Introductionmentioning

confidence: 99%

TEMPO-Assisted Free-Radical-Initiated Peptide Sequencing Mass Spectrometry for Ubiquitin Ions: An Insight on the Gas-Phase Conformations

Lee

Park

et al. 2022

J. Am. Soc. Mass Spectrom.

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TEMPO ((2,2,6,6-tetramethylpiperidine-1-yl)oxyl)-assisted free-radical-initiated peptide sequencing mass spectrometry (FRIPS MS) is applied to the top-down tandem mass spectrometry of guanidinated ubiquitin (UB(Gu)) ions, i.e., p-TEMPO–Bn–Sc–guanidinated ubiquitin (UBT(Gu)), to shed a light on gas-phase ubiquitin conformations. Thermal activation of UBT(Gu) ions produced protein backbone fragments of radical character, i.e., a-/x- and c-/z-type fragments. It is in contrast to the collision-induced dissociation (CID) results for UB(Gu), which dominantly showed the specific charge-remote CID fragments of b-/y-type at the C-terminal side of glutamic acid (E) and aspartic acid (D). The transfer of a radical “through space” was mainly observed for the +5 and +6 UBT(Gu) ions. This provides the information about folding/unfolding and structural proximity between the positions of the incipient benzyl radical site and fragmented sites. The analysis of FRIPS MS results for the +5 charge state ubiquitin ions shows that the +5 charge state ubiquitin ions bear a conformational resemblance to the native ubiquitin (X-ray crystallography structure), particularly in the central sequence region, whereas some deviations were observed in the unstable second structure region (β2) close to the N-terminus. The ion mobility spectrometry results also corroborate the FRIPS MS results in terms of their conformations (or structures). The experimental results obtained in this study clearly demonstrate a potential of the TEMPO-assisted FRIPS MS as one of the methods for the elucidation of the overall gas-phase protein structures.

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“…Bromine's two isotopes create a unique pattern in a mass spectrum of 79Br and 81Br in a 1:1 ratio (79Br, 51%; 81Br, 49%), and this specific isotopic signature readily distinguishes the modified species from unmodified species. Brominated tags were previously used in tandem MS analysis to identify phosphorylation sites 28 and facilitate de novo sequencing 29 and protein identification. 30 Bertozzi et al leveraged the ability to search for distinguishable isotopic signatures and developed a pattern search algorithm known as isotopic signature transfer and mass pattern prediction (IsoStamp) to screen for the precursor ions of modified species, 31 but IsoStamp still faces the challenges of MS limitations and can be prone to false positives and negatives.…”

Section: ■ Introductionmentioning

confidence: 99%

Detection of Alkynes via Click Chemistry with a Brominated Coumarin Azide by Simultaneous Fluorescence and Isotopic Signatures in Mass Spectrometry

et al. 2017

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Alkynes are a key component of click chemistry and used for a wide variety of applications including bioconjugation, selective tagging of protein modifications, and labeling of metabolites and drug targets. However, challenges still exist for detecting alkynes because most 1,2,3-triazole products from alkynes and azides do not possess distinct intrinsic properties that can be used for their facile detection by either fluorescence or mass spectrometry. To address this critical need, a novel brominated coumarin azide was used to tag alkynes and detect alkyne-conjugated biomolecules. This tag has several useful properties: first, it is fluorogenic and the click-chemistry products are highly fluorescent and quantifiable; second, its distinct isotopic pattern facilitates identification by mass spectrometry; and third, its click-chemistry products form a unique pair of reporter ions upon fragmentation that can be used for the quick screening of data. Using a monoclonal antibody conjugated with alkynes, a general workflow has been developed and examined comprehensively.

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Bromine isotopic signature facilitates de novo sequencing of peptides in free‐radical‐initiated peptide sequencing (FRIPS) mass spectrometry

Cited by 9 publications

References 77 publications

Tautomerization and Dissociation of Molecular Peptide Radical Cations

Tautomerization and Dissociation of Molecular Peptide Radical Cations

TEMPO-Assisted Free-Radical-Initiated Peptide Sequencing Mass Spectrometry for Ubiquitin Ions: An Insight on the Gas-Phase Conformations

Detection of Alkynes via Click Chemistry with a Brominated Coumarin Azide by Simultaneous Fluorescence and Isotopic Signatures in Mass Spectrometry

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