An enhanced protein crosslink identification strategy using CID-cleavable chemical crosslinkers and LC/MS n analysis

Fan Liu, Cong Wu, Jonathan V. Sweedler, Michael B. Goshe

Research output: Contribution to journalComment/debate


We describe a novel two-step LC/MS n strategy to effectively and confidently identify numerous crosslinked peptides from complex mixtures. This method incorporates the use of our gas-phase cleavable crosslinking reagent, disuccinimidyl-succinamyl-aspartyl-proline (SuDP), and a new data-processing algorithm CXLinkS (Cleavable Crosslink Selection), which enables unequivocal crosslink peptide selection and identification on the basis of mass measurement accuracy, high resolving power, and the unique fragmentation pattern of each crosslinked peptide. We demonstrate our approach with well-characterized monomeric and multimeric protein systems with and without database searching restrictions where inter-peptide crosslink identification is increased 8-fold over our previously published data-dependent LC/MS 3 method and discuss its applicability to other CID-cleavable crosslinkers and more complex protein systems.

Original languageEnglish (US)
Pages (from-to)401-405
Number of pages5
Issue number3
StatePublished - Feb 1 2012



  • CID-cleavable crosslinker
  • Crosslinking
  • Mass measurement accuracy
  • Multistage CID
  • Protein-protein interactions
  • Technology

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry

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