The influence of histidine on cleavage C-terminal to acidic residues in doubly protonated tryptic peptides

An ion-trap CID MS/MS spectral database of 505 doubly protonated tryptic peptides was used to investigate the influence of an internal basic residue on preferential fragmentation C-terminal to the acidic amino acid residues, aspartic acid (Asp) and glutamic acid (Glu). Because tryptic peptides, which contain C-terminal Lys or Arg, were selected for analysis, the majority of the peptides contain His as the internal basic residue. A comparison between spectra for peptides that do and do not contain an internal basic residue shows that cleavage is more prominent at Asp-Xxx bonds for peptides that do contain the internal basic residue. This result corroborates a previously published mechanism for Asp-Xxx cleavage that states that cleavage at Asp-Xxx is enhanced when protons are sequestered at basic sites, allowing the acidic hydrogen of the Asp side chain to initiate cleavage. The data suggest that in doubly-charged His-containing tryptic peptides, one proton is typically located at the C-terminal Arg or Lys while the mobility of the second proton is hindered by the His side chain’s relatively high basicity. The same investigation was performed for cleavage at Glu-Xxx amide bonds, but in this case there is only a marginal difference between peptides that do and do not contain the internal basic residue. (Int J Mass Spectrom 219 (2002) 233–244) © 2002 Elsevier Science B.V. All rights reserved.