Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

  • Brett Harper
  • Mahsan Miladi
  • Touradj SoloukiEmail author
Research Article


It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAHAA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-“like” ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.


Collision-induced dissociation (CID) Ion mobility spectrometry (IMS) Mass spectrometry (MS) Peptide fragmentation Sequence-scrambling y Fragment 



The authors thank Baylor University for financial support. They also thank Dr. Behrooz Zekavat for helpful discussions of IM-MS and MSn data reported in this manuscript.

Supplementary material

13361_2014_955_MOESM1_ESM.docx (313 kb)
ESM 1 (DOCX 312 kb)


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© American Society for Mass Spectrometry 2014

Authors and Affiliations

  1. 1.Institute of Biomedical StudiesBaylor UniversityWacoUSA
  2. 2.Department of Chemistry and BiochemistryBaylor UniversityWacoUSA

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