Collision-Induced Dissociations of Deprotonated Peptides. Dipeptides Containing Asn, Arg and Lys

Waugh, RJ; Bowie, J. H.; Ml, Gross

doi:10.1071/ch9930693

Cited by 20 publications

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“…A comparison of the low-energy CID results with the high-energy CID results reported by Eckersley et al [12] showed that more extensive and sequence-specific fragmentation was observed in the low-energy CID experiments. This observation is in line with earlier work in this laboratory [20 -23] which showed that low-energy collisional activation of negative ions imparted, on average, greater energy to the anion than did high-energy collisional activationThe early studies [7][8][9][10][11][12][13][14][15][16][17][18] …”

supporting

confidence: 81%

“…On the other hand much less is known concerning the fragmentation modes of deprotonated peptides. The majority of studies [7][8][9][10][11][12][13][14][15][16][17][18] have involved high-energy collision-induced dissociation (CID) and have been largely restricted to the [M Ϫ H] Ϫ ions of dipeptides with only a few tripeptides having been studied.A recent paper from this laboratory [19] has reported the low-energy CID of the [M Ϫ H] Ϫ ions of a variety of dipeptides to pentapeptides containing H or alkyl ␣-groups. The fragmentation reactions observed are illustrated schematically in Scheme 1 using nomenclature adapted from that used [6,7] for fragmentation of protonated peptides.…”

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confidence: 99%

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Effect of phenylalanine on the fragmentation of deprotonated peptides

Harrison

2002

J. Am. Soc. Mass Spectrom.

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The fragmentation reactions of a variety of deprotonated dipeptides and tripeptides containing phenylalanine have been studied using energy-resolved collision-induced dissociation, isotopic labeling and MS/MS/MS experiments. The benzyl ␣-group has a substantial effect on the fragmentation reactions observed. When the phenylalanine is in the C-terminal position of dipeptides or tripeptides a major fragmentation reaction is elimination of neutral cinnamic acid to from a deprotonated amino acid amide (c 1 ion) for dipeptides and a deprotonated dipeptide amide (c 2 ion) for tripeptides. As a result of many studies, the main features of the fragmentation of protonated peptides have been elucidated, at least at the phenomenological level [5,6]. On the other hand much less is known concerning the fragmentation modes of deprotonated peptides. The majority of studies [7][8][9][10][11][12][13][14][15][16][17][18] have involved high-energy collision-induced dissociation (CID) and have been largely restricted to the [M Ϫ H] Ϫ ions of dipeptides with only a few tripeptides having been studied.A recent paper from this laboratory [19] has reported the low-energy CID of the [M Ϫ H] Ϫ ions of a variety of dipeptides to pentapeptides containing H or alkyl ␣-groups. The fragmentation reactions observed are illustrated schematically in Scheme 1 using nomenclature adapted from that used [6,7] for fragmentation of protonated peptides. A comparison of the low-energy CID results with the high-energy CID results reported by Eckersley et al. [12] showed that more extensive and sequence-specific fragmentation was observed in the low-energy CID experiments. This observation is in line with earlier work in this laboratory [20 -23] which showed that low-energy collisional activation of negative ions imparted, on average, greater energy to the anion than did high-energy collisional activationThe early studies [7][8][9][10][11][12][13][14][15][16][17][18] of small deprotonated peptides suggested that the fragmentation modes of the [M Ϫ H]Ϫ ions depended significantly on the identity of the ␣-groups of the constituent amino acids. The present work reports a study of the low-energy CID of deprotonated peptides containing phenylalanine in order to evaluate the role of the benzyl ␣-group on the fragmentation of the deprotonated peptides. The fragmentation reactions of a number of deprotonated dipeptides and two tripeptides containing phenylalanine have been examined by high-energy CID by Waugh et al. [15]. A comparison will be made of the high-energy and low-energy CID results. ExperimentalCollision-induced dissociation (CID) studies were performed using an electrospray/quadrupole mass spectrometer (VG Platform, Micromass, Manchester, UK) with CID in the interface region between the atmospheric pressure source and the quadrupole mass analyzer. It is well known [24,25] that CID can be achieved in this interface region, so-called cone voltage CID, and it has been clearly established [26 -28] that the average energy imparted to the decomposing i...

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supporting

confidence: 81%

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confidence: 99%

Effect of phenylalanine on the fragmentation of deprotonated peptides

Harrison

2002

J. Am. Soc. Mass Spectrom.

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“…In addition, abundant c 4 − is produced although its intensity is generally lower than that of [M − H − NH 3 ] − and [M − H −42] − . Loss of NHCNH from arginine residues in deprotonated peptides has previously been observed by high‐energy CID24 and PSD 22. In addition, no preferential cleavage occurs adjacent to the arginine; this residue does not influence the dissociation pathways of [M − H] − .…”

Section: Resultsmentioning

confidence: 59%

“…However, the peptides in the PSD study generally had many types of residues, making it difficult to elucidate how the basic residues themselves were affecting fragmentation. In addition, Bowie and coworkers23, 24 have shown that b‐ and y‐ions are primarily produced from high‐energy collision‐induced dissociation (CID) of small deprotonated peptides containing histidine, lysine and arginine. Interestingly, these spectra did not contain the c n − series that was seen by PSD 22…”

Section: Introductionmentioning

confidence: 99%

A comparison of positive and negative ion collision‐induced dissociation for model heptapeptides with one basic residue

Pu¹,

Clipston²,

Cassady³

2010

J. Mass Spectrom.

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The effects of the identity and position of basic residues on peptide dissociation were explored in the positive and negative modes. Low-energy collision-induced dissociation (CID) was performed on singly protonated and deprotonated heptapeptides of the type: XAAAAAA, AAAXAAA, AAAAAXA and AAAAAAX, where X is arginine (R), lysine (K) or histidine (H) residues and A is alanine. For [M + H](+), the CID spectra are dominated by cleavages adjacent to the basic residues and the majority of the product ions contain the basic residues. The order of a basic residue's influence on fragmentation of [M + H](+) is arginine > histidine approximately lysine, which is also the order of decreasing gas-phase basicity for these amino acids. These results are consistent with the side chains of basic residues being positive ion charge sites and with the more basic arginine residues having a higher retention (i.e. sequestering) of the positive charge. In contrast, for [M-H](-) the identity and position of basic residues has almost no effect on backbone fragmentation. This is consistent with basic residues not being negative mode charge sites. For these peptides, more complete series of backbone fragments, which are important in the sequencing of unknowns, can be found in the negative mode. Spectra at both polarities contain C-terminal y-ions, but y(n)''(+) has two more hydrogens than the corresponding y(n)(-). Another major difference is the production of the N-terminal backbone series b(n)(+) in the positive mode and c(n)(-) in the negative mode. Thus, comparison of positive and negative ion spectra with an emphasis on searching for pairs of ions that differ by 2 Da (y(n)''(+) vs y(n)(-)) and by 15 Da (b(n)(+) vs c(n)(-)) may be a useful method for determining whether a product ion is generated from the C-terminal or the N-terminal end of a peptide. In addition, a characteristic elimination of NH=C=NH from arginine residues is observed for deprotonated peptides.

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“…Another example of side chain deprotonation was observed by Grzetic and Oomens via IRMPD 33 as well as Bowie and co-workers by CID on asparagine-containing peptides. 10,34 Both groups proposed a succinamide structure that deprotonates at the asparagine side chain and allows charge-directed backbone cleavage.…”

Section: ■ Introductionmentioning

confidence: 99%

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides

et al. 2015

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Using proton-transfer reactions in a Fourier transform ion cyclotron resonance mass spectrometer and correlated molecular orbital theory at the G3(MP2) level, gas-phase acidities (GAs) and the associated structures for amides corresponding to the common amino acids have been determined for the first time. These values are important because amino acid amides are models for residues in peptides and proteins. For compounds whose most acidic site is the C-terminal amide nitrogen, two ions populations were observed experimentally with GAs that differ by 4-7 kcal/mol. The lower energy, more acidic structure accounts for the majority of the ions formed by electrospray ionization. G3(MP2) calculations predict that the lowest energy anionic conformer has a cis-like orientation of the [-C(═O)NH](-) group whereas the higher energy, less acidic conformer has a trans-like orientation of this group. These two distinct conformers were predicted for compounds with aliphatic, amide, basic, hydroxyl, and thioether side chains. For the most acidic amino acid amides (tyrosine, cysteine, tryptophan, histidine, aspartic acid, and glutamic acid amides) only one conformer was observed experimentally, and its experimental GA correlates with the theoretical GA related to side chain deprotonation.

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Collision-Induced Dissociations of Deprotonated Peptides. Dipeptides Containing Asn, Arg and Lys

Cited by 20 publications

References 0 publications

Effect of phenylalanine on the fragmentation of deprotonated peptides

Effect of phenylalanine on the fragmentation of deprotonated peptides

A comparison of positive and negative ion collision‐induced dissociation for model heptapeptides with one basic residue

An Experimental and Computational Study of the Gas-Phase Acidities of the Common Amino Acid Amides

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