Journal of The American Society for Mass Spectrometry

, Volume 30, Issue 9, pp 1631–1642 | Cite as

ETD-Cleavable Linker for Confident Cross-linked Peptide Identifications

  • Bingqing Zhao
  • Colin P. Reilly
  • James P. ReillyEmail author
Research Article


Peptide cross-links formed using the homobifunctional-linker diethyl suberthioimidate (DEST) are shown to be ETD-cleavable. DEST has a spacer arm consisting of a 6-carbon alkyl chain and it cleaves at the amidino groups created upon reaction with primary amines. In ETD MS2 spectra, DEST cross-links can be recognized based on mass pairs consisting of peptide-NH2 and peptide+linker+NH3 ions, and backbone cleavages are more equally distributed over the two constituent peptides compared with collisional activation. Dead ends that are often challenging to distinguish from cross-links are diagnosed by intense reporter ions. ETD mass pairs can be used in MS3 experiments to confirm cross-link identifications. These features provide a simple but reliable approach to identify cross-links that should facilitate studies of protein complexes.


Cross-linking Electron transfer dissociation 



We would like to thank Dr. Jonathan Meek for the spectrum plotting program. This work was supported by the National Institutes of Health grants R01 GM103725 and U54 GM074807. It was partially funded by the Indiana University Vice Provost for Research through the Faculty Research Support Program.

Supplementary material

13361_2019_2227_MOESM1_ESM.docx (721 kb)
ESM 1 (DOCX 721 kb)


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© American Society for Mass Spectrometry 2019

Authors and Affiliations

  1. 1.Department of ChemistryIndiana UniversityBloomingtonUSA

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