Focus: Mobile Proton Model

Journal of the American Society for Mass Spectrometry

, Volume 21, Issue 8, pp 1352-1363

First online:

Effect of the his residue on the cyclization of b ions

  • Benjamin J. BythellAffiliated withComputational Proteomics Group, German Cancer Research Center (DKFZ)
  • , Michaela Knapp-MohammadyAffiliated withDivision of Functional Genome Analysis, German Cancer Research Center (DKFZ)
  • , Béla PaizsAffiliated withComputational Proteomics Group, German Cancer Research Center (DKFZ) Email author 
  • , Alex G. HarrisonAffiliated withDepartment of Chemistry, University of Toronto Email author 


The MSn spectra of the [M + H]+ and b 5 peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b 4 ions derived from the first four peptides. The MS2 spectra of the [M + H]+ ions show a substantial series of bn ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b tons when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b 4 and b 5 ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for b n ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b 5 structures, the b 4 ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b 4 and b 5 the energetically most favored structure is a macrocyclic isomer protonated at the His side chain.