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Evidence for Sequence Scrambling in Collision-Induced Dissociation of y-Type Fragment Ions

  • Research Article
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Journal of The American Society for Mass Spectrometry

Abstract

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.

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Acknowledgment

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 [44] for their thoughtful comments and questions that led us to explore y-fragment ion scramblings.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76798, USA

    Mahsan Miladi & Touradj Solouki

  2. Institute of Biomedical Studies, Baylor University, Waco, TX, 76798, USA

    Brett Harper

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  1. Mahsan Miladi
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  2. Brett Harper
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Correspondence to Touradj Solouki.

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Miladi, M., Harper, B. & Solouki, T. Evidence for Sequence Scrambling in Collision-Induced Dissociation of y-Type Fragment Ions. J. Am. Soc. Mass Spectrom. 24, 1755–1766 (2013). https://doi.org/10.1007/s13361-013-0714-x

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