Bifurcating fragmentation behavior of gas-phase tryptic peptide dications in collisional activation

Collision-activated dissociation (CAD) of tryptic peptides is a cornerstone of mass spectrometry-based proteomics research. Principal component analysis of a database containing 15,000 high-resolution CAD mass spectra of gas-phase tryptic peptide dications revealed that they fall into two classes with a good separation between the classes. The main factor determining the class identity is the relative abundance of the peptide bond cleavage after the first two N-terminal residues. A possible scenario explaining this bifurcation involves trans- to cis-isomerization of the N-terminal peptide bond, which facilitates solvation of the N-terminal charge on the second backbone amide and formation of stable b(2) ions in the form of protonated diketopiperazines. Evidence supporting this scenario is derived from statistical analysis of the high-resolution CAD MS/MS database. It includes the observation of the strong deficit of a(3) ions and anomalous amino acid preferences for b(2) ion formation.