The mobile proton hypothesis in fragmentation of protonated peptides: A perspective

Boyd, Robert K.; Somogyi, Árpád

doi:10.1016/j.jasms.2010.04.017

Cited by 126 publications

(145 citation statements)

References 34 publications

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“…This would lead to the formation of a cyclic imine fused to the peptide backbone (Scheme 1). According to the mobile proton model [11,12,44,45], the collisionally activated protonated peptides would have protonation at all the possible sites (hetero atoms) including the backbone carbonyls of the amides. The Scheme 1 shows that the side chain lysine amine acts as the nucleophile and the carbon center of one of the carbonyl groups of the peptide backbone acts as an electrophile on protonation of the amide carbonyl oxygen.…”

Section: Neutral Loss Of Watermentioning

confidence: 99%

“…Such seven member cyclic imine involving the lysine residue has been suggested to be formed by water loss from the peptide ion (Scheme S1B in the Supporting Information). Scheme 3 shows that the b 8 -ion may exist in an oxazolone [15] structure with the charge (proton) delocalized on the whole peptide ion [11,45]. Protonation of the carbonyl oxygen of a lysine residue would enhance the electrophilicity of the amide carbon and allow formation of the seven membered cyclic intermediate A on nucleophilic attack of the amide carbon by the free ε-NH 2 of the same lysine residue.…”

Section: Deletion Of Internal Lysine Residuementioning

confidence: 99%

“…The collisional excitation of the protonated peptide leads to transfer the ionizing proton from an unreactive site of higher gas-phase basicity (e.g., Arg, Lys, and His side chain or N-terminal α-NH 2 group) to energetically less favored and reactive backbone-amide(s) and carbonyl(s) in the mobile proton model [11,12]. Fast proton transfer to various backbone amide bonds results in the formation of the primary fragment ions e.g.…”

Section: Introductionmentioning

confidence: 99%

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Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

Banerjee

Mazumdar

2012

J. Am. Soc. Mass Spectrom.

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The gas-phase peptide ion fragmentation chemistry is always the center of attraction in proteomics to analyze the amino acid sequence of peptides and proteins. In this work, we describe the formation of an anomalous fragment ion, which corresponds to the selective deletion of the internal lysine residue from a series of lysine containing peptides upon collisional activation in the ion trap. We detected several water-loss fragment ions and the maximum number of water molecules lost from a particular fragment ion was equal to the number of lysine residues in that fragment. As a consequence of this water-loss phenomenon, internal lysine residues were found to be deleted from the peptide ion. The N,N-dimethylation of all the amine functional groups of the peptide stopped the internal lysine deletion reaction, but selective Nterminal α-amino acetylation had no effect on this process indicating involvement of the side chains of the lysine residues. The detailed mechanism of the lysine deletion was investigated by multistage CID of the modified and unmodified peptides, by isotope labeling and by energy resolved CID studies. The results suggest that the lysine deletion might occur through a unimolecular multistep mechanism involving a seven-membered cyclic imine intermediate formed by the loss of water from a lysine residue in the protonated peptide. This intermediate subsequently undergoes degradation reaction to deplete the interior imine ring from the peptide backbone leading to the deletion of an internal lysine residue.

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Section: Neutral Loss Of Watermentioning

confidence: 99%

Section: Deletion Of Internal Lysine Residuementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

Banerjee

Mazumdar

2012

J. Am. Soc. Mass Spectrom.

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“…b, a, and y signals. The mobile proton model [2][3][4][5] covers the mobility/sequestering of ionizing protons, which triggers the peptide chain dissociations. These b, a, and y fragment ions that are directly related to the primary polyamide skeleton are used to deduce the amino acid sequence.…”

Section: Introductionmentioning

confidence: 99%

“…However, it appeared that such residue exclusion only occurred when three conditions were simultaneously satisfied: (1) the precursor ion must be singly charged; (2) a basic residue must be present in the sequence; (3) the Cterminal backbone function must be a carboxylic acid. Within the frame of the mobile proton model [2][3][4][5], provided that at least one of the ionizing protons is sufficiently mobile to be intramolecularly transferred onto any amide bond along the peptide backbone, multiple peptide bond ruptures will be triggered in MS/MS experiments upon precursor ion activation. These competitive fragmentation pathways led to series of ions related to the Nterminal part of the peptide (b/a ions) and C-terminal end (y ions) allowing efficient sequencing.…”

Section: Introductionmentioning

confidence: 99%

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

Dupré

Cantel

Martinez

et al. 2011

J. Am. Soc. Mass Spectrom.

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By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (b n-1 +H 2 O) ion, corresponding to a shortened nonscrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure.The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H 2 O and NH 3 ) and multiple backbone amide ruptures (b-type internal ions), the described Cterminal residue exclusion is highly identifiable giving raise to a single fragment ion in the high mass range of the MS/MS spectra. The mass difference between this signal and the protonated molecular ion corresponds to the mass of the C-terminal residue. It allowed a straightforward identification of the amino acid positioned at this extremity. It must be emphasized that a neutral residue loss can be misattributed to the formation of a y m-1 ion, i.e., to the loss of the N-terminal residue following the a 1 -y m-1 fragmentation channel. Extreme caution must be adopted when reading the direct sequence ion on the positive ion MS/MS spectra of singly charged peptides not to mix up the attribution of the N-and C-terminal amino acids. Although such peculiar fragmentation behavior is of obvious interest for de novo peptide sequencing, it can also be exploited in proteomics, especially for studies involving digestion protocols carried out with proteolytic enzymes other than trypsin (Lys-N, Glu-C, and Asp-N) that produce arginine-containing peptides.

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Fragmentation of Even‐Electron Ions

2017

Interpretation of MS‐MS Mass Spectra of Drugs and Pesticides

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The mobile proton hypothesis in fragmentation of protonated peptides: A perspective

Cited by 126 publications

References 34 publications

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

Selective Deletion of the Internal Lysine Residue from the Peptide Sequence by Collisional Activation

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

Fragmentation of Even‐Electron Ions

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