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Related Experiment Videos

Mobile and localized protons: a framework for understanding peptide dissociation.

V H Wysocki1, G Tsaprailis, L L Smith

  • 1Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA. vwysocki@u.arizona.edu

Journal of Mass Spectrometry : JMS
|February 17, 2001
PubMed
Summary

Tandem mass spectrometry peptide sequencing relies on understanding gas-phase fragmentation. This study refines the mobile proton model, explaining enhanced cleavage at aspartic acid and histidine residues during protein identification.

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Area of Science:

  • Analytical Chemistry
  • Biochemistry
  • Proteomics

Background:

  • Tandem mass spectrometry (MS/MS) is crucial for protein identification and peptide sequencing.
  • Peptide fragmentation patterns, specifically b and y ions from amide bond cleavage, are fundamental to MS/MS.
  • Understanding non-canonical fragmentation, or enhanced cleavage, is key to improving sequencing accuracy.

Purpose of the Study:

  • To refine the mobile proton model for peptide fragmentation in MS/MS.
  • To elucidate the mechanisms behind enhanced cleavage at aspartic acid (Asp) and histidine (His) residues.
  • To improve the accuracy of protein identification and peptide sequencing using mass spectrometry.

Main Methods:

  • Utilized surface-induced dissociation (SID) and gas-phase collision-induced dissociation (CID).

Related Experiment Videos

  • Investigated peptide fragmentation under various experimental conditions.
  • Applied the refined mobile proton model to analyze fragmentation pathways.

    • Main Results:

    • Demonstrated enhanced cleavage at Asp residues via side-chain acidic proton initiating C-terminal amide bond cleavage, forming anhydrides.
    • Showed enhanced cleavage at protonated His residues involves side-chain proton transfer and nucleophilic attack, forming cyclic structures.
    • Differentiated mechanisms of enhanced cleavage at acidic (Asp) versus basic (His) residues.

    Conclusions:

    • The mobile proton model successfully explains enhanced peptide fragmentation at Asp and His residues.
    • Specific mechanisms involving side-chain protonation and nucleophilic attack drive enhanced cleavage at these residues.
    • Accurate interpretation of these fragmentation patterns enhances the reliability of peptide sequencing and protein identification in proteomics.