Journal of the American Society for Mass Spectrometry

, Volume 18, Issue 1, pp 113–120

Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides

  • Mikhail M. Savitski
  • Frank Kjeldsen
  • Michael L. Nielsen
  • Roman A. Zubarev
Articles

DOI: 10.1016/j.jasms.2006.09.008

Cite this article as:
Savitski, M.M., Kjeldsen, F., Nielsen, M.L. et al. J Am Soc Mass Spectrom (2007) 18: 113. doi:10.1016/j.jasms.2006.09.008

Abstract

Hydrogen rearrangement is an important process in radical chemistry. A high degree of H· rearrangement to and from ionic fragments (combined occurrence frequency 47% compared with that of ) is confirmed in analysis of 15,000 tandem mass spectra of tryptic peptides obtained with electron capture dissociation (ECD), including previously unreported double H· losses. Consistent with the radical character of H· abstraction, the residue determining the formation rate of z′=z·+H· species is found to be the N-terminal residue in species. The size of the complementary cm fragment turned out to be another important factor, with z′ species dominating over z· ions for m ≤ 6. The H· atom was found to be abstracted from the side chains as well as from α-carbon groups of residues composing the c′ species, with Gln and His in the c′ fragment promoting H· donation and Asp and Ala opposing it. Ab initio calculations of formation energies of ·A radicals (A is an amino acid) confirmed that the main driving force for H· abstraction by z· is the process exothermicity. No valid correlation was found between the N-Cα bond strength and the frequency of this bond cleavage, indicating that other factors than thermochemistry are responsible for directing the site of ECD cleavage. Understanding hydrogen attachment to and loss from ECD fragments should facilitate automatic interpretation ECD mass spectra in protein identification and characterization, including de novo sequencing.

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Copyright information

© American Society for Mass Spectrometry 2007

Authors and Affiliations

  • Mikhail M. Savitski
    • 1
  • Frank Kjeldsen
    • 1
  • Michael L. Nielsen
    • 1
  • Roman A. Zubarev
    • 1
  1. 1.Laboratory for Biological and Medical Mass SpectrometryUppsala UniversityUppsalaSweden