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Influences of Proline and Cysteine Residues on Fragment Yield in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry

  • Research Article
  • Published:
Journal of The American Society for Mass Spectrometry

Abstract

Matrix-assisted laser desorption/ionization in-source decay produces highly informative fragments for the sequencing of peptides/proteins. Among amino acids, cysteine and proline residues were found to specifically influence the fragment yield. As they are both frequently found in small peptide structures for which de novo sequencing is mandatory, the understanding of their specific behaviors would allow useful fragmentation rules to be established. In the case of cysteine, a c•/w fragment pair originating from Xxx–Cys is formed by side-chain loss from the cysteine residue. The presence of a proline residue contributes to an increased yield of ISD fragments originating from N–Cα bond cleavage at Xxx1–Xxx2Pro, which is attributable to the cyclic structure of the proline residue. Our results suggest that the aminoketyl radical formed by MALDI-ISD generally induces the homolytic N–Cα bond cleavage located on the C–terminal side of the radical site. In contrast, N–Cα bond cleavage at Xxx–Pro produces no fragments and the N–Cα bond at the Xxx1–Xxx2Pro bond is alternatively cleaved via a heterolytic cleavage pathway.

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Acknowledgments

D.A. gratefully acknowledges the research fellowship from the Japan Society for the Promotion of Science for Young Scientists (23–10272). N.S. is an Fonds National de la Recherche Scientifique (F.N.R.S.) logistic collaborator. The F.N.R.S. and Walloon Region contributed the mass spectrometry facility funding.

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  1. Daiki Asakawa

    Present address: Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan

Authors and Affiliations

  1. Chemistry Department and GIGA-R, Mass Spectrometry Laboratory, University of Liege, Liege, Belgium

    Daiki Asakawa, Nicolas Smargiasso, Loïc Quinton & Edwin De Pauw

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  1. Daiki Asakawa
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  2. Nicolas Smargiasso
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  3. Loïc Quinton
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  4. Edwin De Pauw
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Correspondence to Daiki Asakawa.

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Asakawa, D., Smargiasso, N., Quinton, L. et al. Influences of Proline and Cysteine Residues on Fragment Yield in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry. J. Am. Soc. Mass Spectrom. 25, 1040–1048 (2014). https://doi.org/10.1007/s13361-014-0868-1

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  • DOI: https://doi.org/10.1007/s13361-014-0868-1

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