Journal ArticleDOI
a2 Ion Derived from Triglycine: An N1-Protonated 4-Imidazolidinone
Udo H. Verkerk,Chi Kit Andy Siu,Jeffrey D. Steill,Houssain El Aribi,Junfang Zhao,Christopher F. Rodriquez,Jos Oomens,Alan C. Hopkinson,K. W. Michael Siu +8 more
TLDR
In this paper, the prototypical a(2) ion generated from protonated triglycine is predominantly a cyclic N-1-protonated 4-imidazolidinone.Abstract:
Fragmentation of protonated peptides in the gas phase constitutes the basis for gas-phase sequencing of peptides using tandem mass spectrometry. Several mechanistic studies have indicated possible loss of b(n) ion sequence information as a consequence of macrocycle formation from internal nucleophilic attacks. Here, we show by infrared multiple-photon dissociation spectroscopy and density functional theory that the prototypical a(2) ion generated from protonated triglycine is predominantly a cyclic N-1-protonated 4-imidazolidinone. Cyclization resulting from internal nucleophilic attacks therefore may be a more general phenomenon than anticipated.read more
Citations
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Cyclization and Rearrangement Reactions of an Fragment Ions of Protonated Peptides
TL;DR: In this paper, the structure and isomerization reactions of the same ions were studied using density functional theory and infrared spectroscopy provided compelling evidence that an ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n).
Journal ArticleDOI
Diagnosing the Protonation Site of b 2 Peptide Fragment Ions using IRMPD in the X–H (X = O, N, and C) Stretching Region
TL;DR: This work reports on the characterization of the protonation site of oxazolone b2 ions formed in collision-induced dissociation (CID) of the doubly protonated tryptic model-peptide YIGSR, and shows that a band at 3445 cm–1, corresponding to the asymmetric N–H stretch of the (nonprotonated) N-terminal NH2 group, is a distinct vibrational signature of the ring-protonations
Journal ArticleDOI
The Extent and Effects of Peptide Sequence Scrambling Via Formation of Macrocyclic b Ions in Model Proteins
Irine S. Saminathan,X. Simon Wang,Yuzhu Guo,Olga Krakovska,Sébastien N. Voisin,Alan C. Hopkinson,K. W. Michael Siu +6 more
TL;DR: The conclusion is that sequence scrambling is unlikely to impact negatively on the accuracy of automated peptide and protein identifications in proteomics.
Journal ArticleDOI
Thermodynamics and Mechanisms of Protonated Diglycine Decomposition: A Computational Study
P. B. Armentrout,A. L. Heaton +1 more
TL;DR: A full computational description of the fragmentation reactions of protonated diglycine (H+GG) is presented, and the mechanism for the combined loss of carbon monoxide and ammonia is explored for the first time.
Journal ArticleDOI
Competition between diketopiperazine and oxazolone formation in water loss products from protonated ArgGly and GlyArg
TL;DR: In this article, a combination of infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry was applied to characterize the water loss, [M+H-H2O](+), product ions from protonated ArgGly and GlyArg.
References
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Journal ArticleDOI
Mass Spectrometry in Proteomics
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Analysis of proteins and proteomes by mass spectrometry
TL;DR: This work states that any human protein can now be identified directly from genome databases on the basis of minimal data derived by mass spectrometry, and that increased automation of sample handling, analysis, and the interpretation of results will generate an avalanche of qualitative and quantitative proteomic data.
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Mobile and localized protons: a framework for understanding peptide dissociation
TL;DR: In this paper, surface-induced dissociation, along with gas-phase collision-induced disociation performed under a variety of conditions, has been used to refine the general'mobile proton' model and to determine how and why enhanced cleavages occur at aspartic acid residues and protonated histidine residues.
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Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model
TL;DR: The relative positions of the ESI/SID fragmentation efficiency curves depend on several parameters which include peptide composition (e.g., presence/absence of a basic amino acid residue) and peptide size.
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Why Are B ions stable species in peptide spectra
TL;DR: It is concluded that the stable configuration is a protonated oxazolone, which is formed by interaction of the developing charge with the N-terminus carbonyl group and that the reacting configuration is the acyclic acylium ion.