Article

Journal of the American Society for Mass Spectrometry

, Volume 21, Issue 4, pp 646-656

Charge remote fragmentation in electron capture and electron transfer dissociation

  • Xiaojuan LiAffiliated withMass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine
  • , Cheng LinAffiliated withMass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine
  • , Liang HanAffiliated withMass Spectrometry Resource, Department of Biochemistry, Boston University School of MedicineDepartment of Chemistry, Boston University
  • , Catherine E. CostelloAffiliated withMass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine
  • , Peter B. O’ConnorAffiliated withMass Spectrometry Resource, Department of Biochemistry, Boston University School of MedicineDepartment of Chemistry, University of Warwick Email author 

Abstract

Secondary fragmentations of three synthetic peptides (human αA crystallin peptide 1-11, the deamidated form of human βB2 crystallin peptide 4-14, and amyloid β peptide 25-35) were studied in both electron capture dissociation (ECD) and electron-transfer dissociation (ETD) mode. In ECD, in addition to c and z· ion formations, charge remote fragmentations (CRF) of z· ions were abundant, resulting in internal fragment formation or partial/entire side-chain losses from amino acids, sometimes several residues away from the backbone cleavage site, and to some extent multiple side-chain losses. The internal fragments were observed in peptides with basic residues located in the middle of the sequences, which was different from most tryptic peptides with basic residues located at the C-terminus. These secondary cleavages were initiated by hydrogen abstraction at the α-, β-, or γ-position of the amino acid side chain. In comparison, ETD generates fewer CRF fragments than ECD. This secondary cleavage study will facilitate ECD/ETD spectra interpretation, and help de novo sequencing and database searching.