Neutral products formed during backbone fragmentations of protonated peptides in tandem mass spectrometry

Cordero, Marcela M.; Houser, John J.; Wesdemiotis, Chrys

doi:10.1021/ac00059a019

Cited by 181 publications

(211 citation statements)

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“…We have described here an investigation of the fragmentation of the model peptide FGGFL that was conducted using extensive 15 N and 2 H labeling and multiple-stage tandem mass spectrometry under lowenergy CID conditions in a quadrupole ion-trap mass spectrometer. Of particular interest in this study was formation and further dissociation of the a 4 and a 4 * (a 4 -NH 3 ) fragments, and apparent rearrangement and scrambling of peptide sequence during multiple-stage CID.…”

Section: Discussionmentioning

confidence: 99%

“…Of particular interest in this study was formation and further dissociation of the a 4 and a 4 * (a 4 -NH 3 ) fragments, and apparent rearrangement and scrambling of peptide sequence during multiple-stage CID. With respect to the retention or elimination of the 15 N labels, the patterns observed indicate that formation of a 4 * can occur through different structures and distinct pathways. For ( 15 N-F)GGFL and FGG( 15 N-F)L, the a 4 * ion population appears as two distinct peaks separated by 1 mass unit.…”

Section: Discussionmentioning

confidence: 99%

“…Fmoc-protected glycine (G), phenylalanine (F), glycine- 15 and leucine (L)-loaded Wang resin were purchased from Sigma Chemical and used as received. Peptides, once cleaved from the resin, were used without subsequent purification in the CID studies.…”

Section: Mass Spectrometrymentioning

confidence: 99%

“…FGGF oxa (the X shorthand notation is used to note an 15 N labeled residue here) loses CO and then 15 NH 3 on the VG pathway to form the a 4 * ion with the FF_GG oxa composition at m/z 364. The m/z 364 fraction of the a 4 * ion population (Figure 3e) fragments by losing CO to form a 4 *-CO and by eliminating F to form m/z 217 (formation of the ion at m/z 222 will be discussed separately in section 3.2).…”

Section: Cid and Fragmentation Pathways Of Fggflmentioning

confidence: 99%

“…Multiple-stage CID of unlabeled FGGFL, and versions of the peptide bearing 15 N and ␣-d 2 isotope labels, were used to examine the fragmentation and in particular the apparent rearrangement of sequence of this model peptide. This specific sequence was chosen as a good compromise between reproduction of past CID results for YGGFL and reasonable cost of synthesis of a series of isotope labeled peptides.…”

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confidence: 99%

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Structure and reactivity of a_n and a*_n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Bythell

Molesworth

Osburn

et al. 2008

J. Am. Soc. Mass Spectrom.

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Extensive 15 N labeling and multiple-stage tandem mass spectrometry were used to investigate the fragmentation pathways of the model peptide FGGFL during low-energy collisioninduced-dissociation (CID) in an ion-trap mass spectrometer. Of particular interest was formation of a 4 from b 4 and a 4 * (a 4 -NH 3 ) from a 4 ions correspondingly, and apparent rearrangement and scrambling of peptide sequence during CID. It is suggested that the original FGGF oxa b 4 structure undergoes b-type scrambling to form GGFF oxa . These two isomers fragment further by elimination of CO and 14 NH 3 or 15 NH 3 to form the corresponding a 4 and a 4 * isomers, respectively. For ( 15 N-F)GGFL and FGG( 15 N-F)L the a 4 * ion population appears as two distinct peaks separated by 1 mass unit. These two peaks could be separated and fragmented individually in subsequent CID stages to provide a useful tool for exploration of potential mechanisms along the a 4 ¡ a 4 * pathway reported previously in the literature . In most MS/MS experiments, protonated peptides are excited collisionally to induce dissociation (collision-induced-dissociation, CID) and the fragment ion spectrum is used to elucidate peptide sequences. The CID spectra of peptides in proteomics studies are commonly assigned by bioinformatics tools that implement sequencing algorithms and peptide fragmentation models. Regrettably, the existing sequencing programs are based on rather limited fragmentation models that poorly approximate the rich dissociation chemistry of protonated peptides [3]. These limitations often lead to erroneous assignment of peptides and proteins, and the resulting uncertainty in the evaluation of the raw MS/MS data is one of the major limiting factors in large-scale protein identification studies [4,5]. The incorporation of more detailed peptide fragmentation mechanisms and spectral characteristics into these sequencing algorithms would undoubtedly place MS/MS based sequencing on a much more robust basis.In general, fragmentation of protonated peptides under low-energy collision conditions involves protondriven reactions in which amide bonds are cleaved along the peptide backbone and b, y, and a ions [6,7] are formed. The energetics and kinetics of the necessary proton mobilization (mobile proton model [8,9]) and amide bond cleavage pathways [3, 10 -14] have received significant research interest. On the other hand, much less attention has been devoted to the structure and reactivity of the primary fragments formed by backbone cleavages. According to the recent pathways in competition (PIC) fragmentation model [3], the thermodynamic properties and the reactivity of these fragAddress reprint requests to Dr. M. Van Stipdonk,

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Mass Spectrometrymentioning

confidence: 99%

Section: Cid and Fragmentation Pathways Of Fggflmentioning

confidence: 99%

mentioning

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Structure and reactivity of a_n and a*_n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Bythell

Molesworth

Osburn

et al. 2008

J. Am. Soc. Mass Spectrom.

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Specific fragmentation of thioxo peptides facilitates the assignment of the thioxylated amino acid

et al. 1997

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Low‐energy collision‐induced dissociation (CID) product ion spectra of a series of singly protonated thioxo peptides produced by electrospray ionization (ESI) were obtained by triple‐quadrupole tandem mass spectrometry. The principal feature of the spectra is a preferential cleavage of the peptide bond succeeding the thioxo peptide moiety. Thus this method provides the possibility of assigning the position of the thioxylated amino acid in oligopeptides resulting from the thioxylation procedure with Lawesson’s or a related reagent. At low collision energy, dominant B ions and/or complementary Y″ ions are observed. Higher collision energy yields internal ions that consist of two adjacent amino acids encompassing the thioxo peptide bond. The formation of these internal ions and the elimination of CO from them give evidence for the position of the thioxylated amino acid. There are strong indications of a stabilization of the B and internal ions through the formation of a thiazolone. Fragment ions resulting from the cleavage of the thioxo peptide bond are either completely absent or of very low intensity. © 1997 John Wiley & Sons, Ltd.

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Specific fragmentation of thioxo peptides facilitates the assignment of the thioxylated amino acid

Pfeifer¹,

Schierhorn²,

Friedemann³

et al. 1997

J. Mass Spectrom.

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Low-energy collision-induced dissociation (CID) product ion spectra of a series of singly protonated thioxo peptides produced by electrospray ionization (ESI) were obtained by triple-quadrupole tandem mass spectrometry. The principal feature of the spectra is a preferential cleavage of the peptide bond succeeding the thioxo peptide moiety. Thus this method provides the possibility of assigning the position of the thioxylated amino acid in oligopeptides resulting from the thioxylation procedure with LawessonÏs or a related reagent. At low collision energy, dominant B ions and/or complementary Y/ ions are observed. Higher collision energy yields internal ions that consist of two adjacent amino acids encompassing the thioxo peptide bond. The formation of these internal ions and the elimination of CO from them give evidence for the position of the thioxylated amino acid. There are strong indications of a stabilization of the B and internal ions through the formation of a thiazolone. Fragment ions resulting from the cleavage of the thioxo peptide bond are either completely absent or of very low intensity.

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Neutral products formed during backbone fragmentations of protonated peptides in tandem mass spectrometry

Cited by 181 publications

References 12 publications

Structure and reactivity of a_n and a*_n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Structure and reactivity of a_n and a*_n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Specific fragmentation of thioxo peptides facilitates the assignment of the thioxylated amino acid

Specific fragmentation of thioxo peptides facilitates the assignment of the thioxylated amino acid

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Neutral products formed during backbone fragmentations of protonated peptides in tandem mass spectrometry

Cited by 181 publications

References 12 publications

Structure and reactivity of an and a*n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Structure and reactivity of an and a*n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Specific fragmentation of thioxo peptides facilitates the assignment of the thioxylated amino acid

Specific fragmentation of thioxo peptides facilitates the assignment of the thioxylated amino acid

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Structure and reactivity of a_n and a*_n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations

Structure and reactivity of a_n and a*_n peptide fragments investigated using isotope labeling, tandem mass spectrometry, and density functional theory calculations