Leveraging Gas-Phase Fragmentation Pathways for Improved Identification and Selective Detection of Targets Modified by Covalent Probes

Anal Chem. 2016 Dec 20;88(24):12248-12254. doi: 10.1021/acs.analchem.6b03394. Epub 2016 Nov 30.


The recent approval of covalent inhibitors for multiple clinical indications has reignited enthusiasm for this class of drugs. As interest in covalent drugs has increased, so too has the need for analytical platforms that can leverage their mechanism-of-action to characterize modified protein targets. Here we describe novel gas phase dissociation pathways which yield predictable fragment ions during MS/MS of inhibitor-modified peptides. We find that these dissociation pathways are common to numerous cysteine-directed probes as well as the covalent drugs, Ibrutinib and Neratinib. We leverage the predictable nature of these fragment ions to improve the confidence of peptide sequence assignment in proteomic analyses and explore their potential use in selective mass spectrometry-based assays.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Cell Line, Tumor
  • Drug Discovery / methods
  • Humans
  • Molecular Targeted Therapy
  • Peptides / analysis*
  • Peptides / metabolism
  • Protein Kinase Inhibitors / pharmacology*
  • Protein Kinases / chemistry
  • Protein Kinases / metabolism
  • Proteomics / methods*
  • Pyrazoles / pharmacology*
  • Pyrimidines / pharmacology*
  • Quinolines / pharmacology*
  • Tandem Mass Spectrometry / methods*


  • Peptides
  • Protein Kinase Inhibitors
  • Pyrazoles
  • Pyrimidines
  • Quinolines
  • ibrutinib
  • Protein Kinases
  • neratinib