Intrinsic Amino Acid Size Parameters from a Series of 113 Lysine-Terminated Tryptic Digest Peptide Ions

Valentine, Stephen J.; Counterman, Anne E.; Hoaglund-Hyzer, Cherokee S.; Clemmer, David E.

doi:10.1021/jp983906o

Cited by 72 publications

(89 citation statements)

References 19 publications

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“…The total recombination energies depend on the conformation of the peptide ions. Valentine et al [53] calculated that peptide ions of the form [(Xxx) n -Lys ϩ H] ϩ have very similar cross sections to the analogous [(Xxx) n -Arg ϩ H] ϩ ions. If the same is true of doubly charged species, and then the recombination energy would be greater for the Lys-containing peptides than the Arg-containing peptides.…”

Section: Resultsmentioning

confidence: 99%

Investigation of the presence of b ions in electron capture dissociation mass spectra

Cooper

2005

J. Am. Soc. Mass Spectrom.

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Previously, we have indicated (Cooper, H.J., et al. Int. J. Mass Spectrom., 2003, 228, 723-728) that electron capture dissociation (ECD) of the doubly protonated peptides, Leu 4 -Sar-Leu 3 -Lys-OH, Leu 4 -Ala-Leu 3 -Lys-OH, Gly 4 -Sar-Gly 3 -Lys-NH 2 , and Gly 3 -Pro-Sar-Gly 3 -Lys-NH 2 , results in abundant b ions, which derive from fragmentation of backbone amide bonds, a nonstandard fragmentation channel in ECD. The instrumental conditions were such that the possibility that collision-induced dissociation processes were contributing to the observed spectra was eliminated. In a separate study (Fung, Y.M.E., et al. Eur. J. Mass Spectrom., 2004, 10, 449 -457. ECD of peptides Arg-(Gly) n -Xxx-(Gly) n -Arg, where Xxx is the amino acid of interest, did not result in b ions. The variation in ECD observed for strikingly similar peptides suggests that the nature of the charge carrier (Arg or Lys) is instrumental in governing the fragmentation channels. Here, we describe the ECD behavior of a suite of model peptides designed such that the nature and position of the charge carrier could be probed. The results suggest that the presence of b ions in ECD spectra is a consequence of both charge carrier and peptide structure. The mechanism by which ECD of NOC␣ bonds in peptides and proteins occurs has been a matter of considerable debate [1, 5, 14 -23]. One proposed mechanism [1] involves capture of an electron by a charged site in the ion, for example, a protonated lysine or arginine residue, followed by H· transfer to (or recapture by) an amide carbonyl resulting in an aminoketyl radical. The radical subsequently dissociates via cleavage of the NOC␣ bond. Originally, it was suggested that c/z· fragment ion formation proceeded faster than vibrational energy redistribution, and that the process was nonergodic [1]. Recent work by Tureček suggests that NOC␣ bond dissociation is particularly facile in thermalized radicals and radical cations, that is, nonergodicity does not apply [21]. McLafferty and coworkers [24] showed that infrared multiphoton dissociation of thermalized [M ϩ 12H] 11ϩ· ions results in the dominant loss of H· atoms in marked contrast to the c/z ions produced following electron capture by [M ϩ 12H] 12ϩ ions to form [M ϩ 12H] 11ϩ· radical ions. These researchers concluded that ECD was nonergodic and the mechanism involves electron capture in a high-n Rydberg state followed by cooling to a dissociative electronic state. A direct mechanism has been suggested in which electron capture at C OH ϩ is accompanied by cleavage of the NOC␣ bond. Uggerud and coworkers [25,26] have shown theoretically and experimentally that both hydrogen transfer and direct processes play a role in ECD. Recently, Syrstad and Tureček [27] have proposed a mechanism for ECD that explains the low selectivity of NOC␣ cleavage and applies equally to peptide ions whose charge carriers are not protons. Either electron capture in a ground electronic state results in hydrogen atom transfer from the ammonium group to the amide carbonyl ...

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Section: Resultsmentioning

confidence: 99%

Investigation of the presence of b ions in electron capture dissociation mass spectra

Cooper

2005

J. Am. Soc. Mass Spectrom.

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“…One IMS-based strategy proposed for improving peptide identification is the utilization of intrinsic size parameters (ISPs) [14, 41–45]. ISPs provide the average value each amino acid residue or modification contributes to a peptide’s cross section.…”

Section: Introductionmentioning

confidence: 99%

“…ISPs provide the average value each amino acid residue or modification contributes to a peptide’s cross section. Therefore, ISPs can be used to predict collision cross sections based on amino acid sequence composition [14, 41–45]. In addition, ISPs provide general insight into peptide structure.…”

Section: Introductionmentioning

confidence: 99%

Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

Glover

Dilger

Acton

et al. 2016

J. Am. Soc. Mass Spectrom.

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Ion mobility spectrometry-mass spectrometry (IMS-MS) techniques are used to study the general effects of phosphorylation on peptide structure. Cross sections for a library of 66 singly phosphorylated peptide ions from 33 pairs of positional isomers, and unmodified analogues were measured. Intrinsic size parameters (ISPs) derived from these measurements yield calculated collision cross sections for 85% of these phosphopeptide sequences that are within ±2.5% of experimental values. The average ISP for the phosphoryl group (0.64 ± 0.05) suggests that in general this moiety forms intramolecular interactions with the neighboring residues and peptide backbone, resulting in relatively compact structures. We assess the capability of ion mobility to separate positional isomers (i.e., peptide sequences that differ only in the location of the modification) and find that more than half of the isomeric pairs have >1% difference in collision cross section. Phosphorylation is also found to influence populations of structures that differ in the cis/trans orientation of Xaa–Pro peptide bonds. Several sequences with phosphorylated Ser or Thr residues located N-terminally adjacent to Pro residues show fewer conformations compared to the unmodified sequences.

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“…Hereinafter Counterman et al [21] performed a successful QSPR study on 103 peptide ions by using several intricate techniques as projection approximation, exact hard sphere scattering and trajectory calculations, indicating that volumes of individual amino acid residues are related significantly with the collision cross section. In Valentine et als works [22] the contributions to peptide collision cross section by different residues of 20 natural amino acids were defined as intrinsic size parameter (ISP). Using this method Shvartsburg et al [23] and Hilderbrand et al [24] systematically investigated the influence of different residues on collision cross section by studying a set of singly protonated Lys-terminated peptide ions.…”

Section: Introductionmentioning

confidence: 99%

Prediction of Ion Drift Times for a Proteome‐Wide Peptide Set Using Partial Least Squares Regression, Least‐Squares Support Vector Machine and Gaussian Process

Liu¹,

Liang²,

Fan³

et al. 2009

QSAR Comb. Sci.

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Quantitative structure-property relationships (QSPRs) have been developed to predict the ion mobility spectrometry (IMS) drift time t D for a set of 1481 peptides generated by protease digestion of the Drosophila melanogaster proteome using information directly derived from molecular structures. The relationship between peptide structure and the drift time t D was constructed by using partial least squares regression (PLS), least-squares support vector machine (LSSVM) and Gaussian process (GP) coupled with genetic algorithm-variable selection. Among these models, the linear PLS was incapable of capturing all dependences in this peptide system; nonlinear LSSVM and GP methods presented a good statistical performance on reproducing peptide mobility behavior. Moreover, since GP was able to handling both linear and nonlinear-hybrid relationship, it gave a stronger fitting ability and a better predictive power than the LSSVM. Systematic analysis of the GP model showed that diversified properties contribute remarkable effect to the relationship between the drift time and the peptide structure. Particularly, the structural topological information and charge distribution contribute significantly to the drift time of peptides.

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Intrinsic Amino Acid Size Parameters from a Series of 113 Lysine-Terminated Tryptic Digest Peptide Ions

Cited by 72 publications

References 19 publications

Investigation of the presence of b ions in electron capture dissociation mass spectra

Investigation of the presence of b ions in electron capture dissociation mass spectra

Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

Prediction of Ion Drift Times for a Proteome‐Wide Peptide Set Using Partial Least Squares Regression, Least‐Squares Support Vector Machine and Gaussian Process

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