N-Protonated Isomers as Gateways to Peptide Ion Fragmentation

Hæffner, Fredrik; Merle, John K.; Irikura, Karl K.

doi:10.1007/s13361-011-0241-6

Cited by 15 publications

(16 citation statements)

References 66 publications

(77 reference statements)

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“…In triglycine, the largest peptide for which gas-phase basicity calculations involving all heteroatoms have been performed, protonation at the internal carbonyl oxygen requires 7 kcal/mol more energy than protonation at the N-terminal carbonyl oxygen [110]. For triglycine (GGG), the C-terminal carboxylate carbonyl oxygen is of comparable basicity to the amide nitrogens [110], which are widely considered to be gas-phase protonation sites in the mobile proton model of peptide dissociation [9,111]. The fact that converting the C-terminus to a methyl ester prevents supercharging may mean that the second proton residues at the C-terminus.…”

Section: Resultsmentioning

confidence: 99%

The Use of Chromium(III) to Supercharge Peptides by Protonation at Low Basicity Sites

Feng

Commodore

Cassady

2014

J. Am. Soc. Mass Spectrom.

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The addition of chromium(III) nitrate to solutions of peptides with seven or more residues greatly increases the formation of doubly protonated peptides, [M+2H]2+, by electrospray ionization. The test compound heptaalanine has only one highly basic site (the N-terminal amino group) and undergoes almost exclusive single protonation using standard solvents. When Cr(III) is added to the solution, abundant [M+2H]2+ forms, which involves protonation of the peptide backbone or the C-terminus. Salts of Al(III), Mn(II), Fe(III), Fe(II), Cu(II), Zn (II), Rh(III), La(III), Ce(IV), and Eu(III) were also studied. While several metal ions slightly enhance protonation, Cr(III) has by far the greatest ability to generate [M+2H]2+. Cr(III) does not supercharge peptide methyl esters, which suggests that the mechanism involves interaction of Cr(III) with a carboxylic acid group. Other factors may include the high acidity of hexaaquochromium(III) and the resistance of Cr(III) to reduction. Nitrate salts enhance protonation more than chloride salts and a molar ratio of 10:1 Cr(III):peptide produces the most intense [M+2H]2+. Cr(III) also supercharges numerous other small peptides, including highly acidic species. For basic peptides, Cr(III) increases the charge state (2+ versus 1+) and causes the number of peptide molecules being protonated to double or triple. Chromium(III) does not supercharge the proteins cytochrome c and myoglobin. The ability of Cr(III) to enhance [M+2H]2+ intensity may prove useful in tandem mass spectrometry because of the resulting overall increase in signal-to-noise ratio, the fact that [M+2H]2+ generally dissociate more readily than [M+H]+, and the ability to produce [M+2H]2+ precursors for electron-based dissociation techniques.

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Section: Resultsmentioning

confidence: 99%

The Use of Chromium(III) to Supercharge Peptides by Protonation at Low Basicity Sites

Feng

Commodore

Cassady

2014

J. Am. Soc. Mass Spectrom.

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“…Knowledge of the energetics and the structural rearrangements taking place during the fragmentation process has proved very valuable in explaining various features of mass spectra of short peptides, e.g., sequence scrambling . A comprehensive review on the topic has been published and more recent developments have been reported …”

Section: Dissociation Energies (Kcal/mol) For Fragmentation Channels mentioning

confidence: 99%

“…However, for longer peptides or peptides with acidic and/or basic side chains, transition states may turn out to be higher than the final states and our method would not be applicable. In this case in order to find the fragmentation propensity at each amide bond, one may analyse the stability of the corresponding N‐protonated isomer, as has been recently proposed …”

Section: Dissociation Energies (Kcal/mol) For Fragmentation Channels mentioning

confidence: 99%

“…[14] A comprehensive review on the topic has been published [15][16][17] and more recent developments have been reported. [18][19][20][21][22][23][24][25][26] There have been, however, few attempts to predict relative intensities of different m/z peaks. These attempts were limited to comparing the probabilities of retaining the charge on one or the other fragments.…”

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confidence: 99%

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Using dissociation energies to predict observability of b‐ and y‐peaks in mass spectra of short peptides

Obolensky,

Wu,

Shen

et al. 2012

Rapid Comm Mass Spectrometry

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RATIONALE Peptide identification reliability can be improved by excluding from analysis those m/z peaks of candidate peptides, which can not be observed in practice due to various physical, chemical or thermodynamic considerations. We propose using dissociation energies (as opposed to proton affinities) as a predictor of observability of different m/z peaks in spectra of short peptides. METHODS Experiment Mass spectra of tetrapeptides AAAA, AAFA, AAVA, AFAA, AVAA, AFFA, AVVA have been measured in the CID activation mode on a grid of activation times 0.05 to 100 ms and normalized collision energy 10 to 35 %. Computations Lowest energy geometries and vibrational spectra were calculated for the precursor ions and their charged and neutral fragments using DFT at the TPSS/6-31G(d,p) level. Dissociation energies were calculated for all fragmentation channels leading to b− or y− fragments. RESULTS It is demonstrated that m/z peaks observed in the mass spectra correspond to the fragmentation channels with the lowest dissociation energies. Using 50 kcal/mol as the cut off value of dissociation energy, it was predicted that 28 out of 42 possible peaks in the b− and y− series of the seven tetrapeptides cab be observed in mass spectra. In the experiments, 26 b− or y− peaks were observed, all of which are among the 28 predicted ones. CONCLUSIONS The use of dissociation energies generalizes the use of proton affinities for semi-quantitative predictions of relative intensities of different m/z peaks of short peptides. Further advances in this direction will pave the way for reliable quantitative predictions and, hence, for a significant improvement in robustness and accuracy of peptide and protein identification tools.

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“…The calculated DFT relative energies include contributions from all these interactions and thus allow one to gauge the relative ion–dipole interactions in a semiquantitative manner and relate them to the major structure features in the optimized structures. The effects of Coulomb interactions on the thermochemistry of multiply charged ions have been addressed previously for non-peptidic [77–79] as well as peptide ions [80, 81]. The pairwise Coulomb energies were estimated from the standard formula, E c (kJ mol −1 ) = Σ1389.38/ R ij , where the distance ( R ij in Å) between the charged groups i and j was measured from the central atoms (N for ammonium and C for guanidinium).…”

Section: Discussionmentioning

confidence: 99%

Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization

Pepin

Laszlo

Marek

et al. 2016

J. Am. Soc. Mass Spectrom.

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Heptapeptide ions containing combinations of polar Lys, Arg, and Asp residues with non-polar Leu, Pro, Ala, and Gly residues were designed to study polar effects on gas-phase ion conformations. Doubly and triply charged ions were studied by ion mobility mass spectrometry and electron structure theory using correlated ab initio and density functional theory methods and found to exhibit tightly folded 3D structures in the gas phase. Manipulation of the basic residue positions in LKGPADR, LRGPADK, KLGPADR, and RLGPADK resulted in only minor changes in the ion collision cross sections in helium. Replacement of the Pro residue with Leu resulted in only marginally larger collision cross sections for the doubly and triply charged ions. Disruption of zwitterionic interactions in doubly charged ions was performed by converting the C-terminal and Asp carboxyl groups to methyl esters. This resulted in very minor changes in the collision cross sections of doubly charged ions and even slightly diminished collision cross sections in most triply charged ions. The experimental collision cross sections were related to those calculated for structures of lowest free energy ion conformers that were obtained by extensive search of the conformational space and fully optimized by density functional theory calculations. The predominant factors that affected ion structures and collision cross sections were due to attractive hydrogen bonding interactions and internal solvation of the charged groups that overcompensated their Coulomb repulsion. Structure features typically assigned to the Pro residue and zwitterionic COO-charged group interactions were only secondary in affecting the structures and collision cross sections of these gas-phase peptide ions.

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N-Protonated Isomers as Gateways to Peptide Ion Fragmentation

Cited by 15 publications

References 66 publications

The Use of Chromium(III) to Supercharge Peptides by Protonation at Low Basicity Sites

The Use of Chromium(III) to Supercharge Peptides by Protonation at Low Basicity Sites

Using dissociation energies to predict observability of b‐ and y‐peaks in mass spectra of short peptides

Toward a Rational Design of Highly Folded Peptide Cation Conformations. 3D Gas-Phase Ion Structures and Ion Mobility Characterization

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