Influence of Size on Apparent Scrambling of Sequence During CID of b-Type Ions

We investigated the influence of peptide size on the apparent loss of sequence during collision-induced dissociation (CID) of b ions using a group of peptides containing from between 4 and 10 residues. Although scrambling of sequence for b 3 + generated from tetrapeptides is minimal, significant formation of nondirect sequence ions (i.e., ions for which scrambling has apparently occurred) was observed for all larger b ions included in the study. Multiple-stage CID experiments demonstrate loss of internal residues and remarkable similarity of product ion spectra among b n ions from permuted sequence isomers. The results support the hypothesis that significant sequence scrambling can occur following fragmentation of b-type ions.