Comparing Mass Spectrometric Characteristics of Peptides and Peptoids

Heerma, W.; Versluis, Cees; Koster, Chris G. de; Kruijtzer, John A. W.; Žigrović, Ivanka; Liskamp, Rob M. J.

doi:10.1002/(sici)1097-0231(19960315)10:4<459::aid-rcm501>3.0.co;2-j

Cited by 34 publications

(21 citation statements)

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“…Therefore, MS/MS was used to obtain more detailed structural information. In the case of peptides and peptoids this method can be used for sequencing, because the fragments that result from CID of the protonated molecular ion [M + H] + are directly related to the peptide or peptoid sequence 23, 24. The proposed nomenclature for the sequence ions of peptoids corresponds to that of peptides (Roepfstorff nomenclature25) and could therefore be used here also for peptoid–peptide hybrids.…”

Section: Resultsmentioning

confidence: 99%

“…This flexibility results from rotation about the tertiary amide bond, which is much less difficult than rotation about a secondary amide bond in (non‐proline‐containing) peptides. Two earlier reports from our laboratories showed that mass spectrometry can play a key role in the unambiguous characterization of peptoids 23, 24. Using the technique of fast atom bombardment ionization combined with high‐energy collision‐induced dissociation (CID) tandem mass spectrometry (MS/MS), spectra of the [M + H] + ions of peptoids and isomeric peptides were compared and found to differ in their relative abundances of Y″‐ and B‐type fragment ions.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of a phosphorylated peptide and peptoid and peptoid–peptide hybrids by mass spectrometry

Ruijtenbeek

Versluis²,

Heck³

et al. 2001

J. Mass Spectrom.

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Nano-electrospray tandem mass spectrometry (nano-ES-MS/MS) was used to record collision-induced dissociation (CID) spectra of a set of peptoid-peptide hybrids and the complete peptoid derived from the phosphopeptide Ac-pTyr-Glu-Thr-Leu-NH(2) (1). The presence of B and Y''-type fragment ions in the tandem mass spectra of the protonated molecular ions [M + H](+) allowed confirmation of sequence similar to mass spectrometric sequence analysis in peptides. In the isomeric peptoid compounds studied, one or several amino acid residues were replaced by peptoid residues (N-substituted glycine residues), which resulted in characteristic tandem mass spectra with differently increased relative abundances of Y''-and B-type fragment ions. The increment of a particular Y''-ion was directly correlated to the position of a peptoid residue present. In addition to these increased peak intensities, other characteristic peaks were also observed compared with the spectrum of reference peptide 1. When a peptoid phosphotyrosine was incorporated, the presence of this residue was apparent from the occurrence of a relatively intense peak at m/z 187 representing the positively charged side-chain of phosphotyrosine, which was almost absent in the spectrum of the reference peptide 1. Since the threonine side-chain had to be translated into the homo peptoid analog this substitution was apparent from the presence of [M + H](+) and fragment ions 14 mass units higher than observed in the spectrum of the reference phosphopeptide 1. The presence of an NLeu peptoid residue could be confirmed by the specific fragmentation of the immonium ion showing an intense peak in its tandem mass spectrum at m/z 57, which results from the loss of an neutral imine molecule leading to a positively charged [C(4)H(9)](+) ion. By means of these mass spectrometric characteristics, all isomeric peptoid compounds could be distinguished from each other and characterized. The methods used appear to be very useful in future studies of peptoids and peptoid-peptide hybrids.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Characterization of a phosphorylated peptide and peptoid and peptoid–peptide hybrids by mass spectrometry

Ruijtenbeek

Versluis²,

Heck³

et al. 2001

J. Mass Spectrom.

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“…Although CA of proton or metal ion-charged peptides generates ions from charge-remote fragmentation and provides some structural information (Johnson et al, 1987;Johnson, Martin & Biemann, 1988;Ishidawa et al, 1994;Summer®eld et al, 1995;Boutin et al, 1996;Heerma et al, 1996), ions from charge-driven chemistry are also formed because the location of the charge on the peptide chain is mobile and dif®cult to predict. Although the resulting spectra are not dif®cult to predict, spectra produced by a single charge-remote process may be simpler to interpret.…”

Section: G Peptidesmentioning

confidence: 99%

Applications and mechanisms of charge-remote fragmentation

Cheng

Gross

2000

Mass Spectrom. Rev.

255

119

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“…Peptoids fragment in a manner similar to that of peptides under CID conditions [41,42,44,47]. The main fragment ions observed correspond to the dissociation of the amide bonds of the peptoid backbone, which produce B-and Y-series ions (following the Roepstorff and Fohlman nomenclature [49]).…”

Section: Nomenclature Of Peptoid Fragment Ionsmentioning

confidence: 99%

“…Tandem mass spectrometry (MS/MS) techniques coupled with either electrospray ionization (ESI) or matrix-assisted laser desorption/ionization (MALDI) are now routinely used for peptide and protein sequencing [34][35][36][37]. These tandem mass spectrometry based techniques have also shown promise as the method of choice for peptoid sequencing [29,[38][39][40][41][42][43][44][45][46]. We have previously studied the fragmentation patterns of a group of protonated and alkali-metallated peptoids under collision-induced dissociation (CID) as well as under electron capture dissociation (ECD) conditions [47,48].…”

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confidence: 99%

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

Ren¹,

Tian²,

Hossain³

et al. 2016

J. Am. Soc. Mass Spectrom.

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Abstract. Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B-versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant Bions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

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Comparing Mass Spectrometric Characteristics of Peptides and Peptoids

Cited by 34 publications

References 1 publication

Characterization of a phosphorylated peptide and peptoid and peptoid–peptide hybrids by mass spectrometry

Characterization of a phosphorylated peptide and peptoid and peptoid–peptide hybrids by mass spectrometry

Applications and mechanisms of charge-remote fragmentation

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

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