Evidence for Sequence Scrambling in Collision-Induced Dissociation of y-Type Fragment Ions
- 342 Downloads
Sequence scrambling from y-type fragment ions has not been previously reported. In a study designed to probe structural variations among b-type fragment ions, it was noted that y fragment ions might also yield sequence-scrambled ions. In this study, we examined the possibility and extent of sequence-scrambled fragment ion generation from collision-induced dissociation (CID) of y-type ions from four peptides (all containing basic residues near the C-terminus) including: AAAAHAA-NH2 (where “A” denotes carbon thirteen (13C1) isotope on the alanine carbonyl group), des-acetylated-α-melanocyte (SYSMEHFRWGKPV-NH2), angiotensin II antipeptide (EGVYVHPV), and glu-fibrinopeptide b (EGVNDNEEGFFSAR). We investigated fragmentation patterns of 32 y-type fragment ions, including y fragment ions with different charge states (+1 to +3) and sizes (3 to 12 amino acids). Sequence-scrambled fragment ions were observed from ~50 % (16 out of 32) of the studied y-type ions. However, observed sequence-scrambled ions had low relative intensities from ~0.1 % to a maximum of ~12 %. We present and discuss potential mechanisms for generation of sequence-scrambled fragment ions. To the best of our knowledge, results on y fragment dissociation presented here provide the first experimental evidence for generation of sequence-scrambled fragments from CID of y ions through intermediate cyclic “b-type” ions.
Key wordsCollision-induced dissociation (CID) Mass spectrometry (MS) Peptide fragmentation Sequence scrambling y Fragment
The Authors thank Baylor University for financial support. They thank Dr. Behrooz Zekvat for helpful discussions on CID data. The authors express their gratitude to reviewers of a previous paper  for their thoughtful comments and questions that led us to explore y-fragment ion scramblings.
- 11.Mujezinovic, N., Raidl, G., Hutchins, J.R., Peters, J.M., Mechtler, K., Eisenhaber, F.: Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. Proteomics 6, 5117–5131 (2006)CrossRefGoogle Scholar
- 21.Fattahi, A., Solouki, T.: Conformational analysis of metal complexed model peptides and their fragment ions using FT-ICR MS and gas-phase H/D exchange reactions. Proceedings of the 49th ASMS Conference on Mass Spectrometry and Allied Topics, Chicago, IL, May 2001Google Scholar
- 35.Solouki, T., Zekavat, B., Miladi, M.: On the existence of structurally different isobaric bn fragment ions. Proceedings of the 58th ASMS Conference on Mass Spectrometry and Allied Topics, Salt Lake City, UT, May 2010Google Scholar