Origin of Product Ions in the MS/MS Spectra of Peptides in a Quadrupole Ion Trap

Stored waveform inverse Fourier transform and double resonance techniques have been used in conjunction with a quadrupole ion trap to study the dissociation patterns of peptide ions. These experiments provide insight into the origin of individual product ions in an MS/MS spectrum. Results show for a series of leucine enkephalin analogues with five amino acid residues that the b 4 ion is the main product ion through which many other product ions arise. It was also observed that the percentage of the a 4 product ions that are formed directly from the protonated molecule (M+H) + depends on the nature of the fourth amino acid residue. In addition, it was determined that in the peptides studied here lower series b ions (e.g., b 3 ) arise from direct dissociation of higher series b ions (e.g., b 4 ) only about 50% of the time.