Mapping Protein-Ligand Interactions with Proteolytic Fragmentation, Hydrogen/Deuterium Exchange-Mass Spectrometry

Methods Enzymol. 2016;566:357-404. doi: 10.1016/bs.mie.2015.08.010. Epub 2015 Oct 23.


Biological processes are the result of noncovalent, protein-ligand interactions, where the ligands range from small organic and inorganic molecules to lipids, nucleic acids, peptides, and proteins. Amide groups within proteins constantly exchange protons with water. When immersed in heavy water (D2O), mass spectrometry (MS) can measure the change of mass associated with the hydrogen to deuterium exchange (HDX). Protein-ligand interactions modify the hydrogen exchange rates of amide protons, and the measurement of the amide exchange rates can provide rich information regarding the dynamical structure of the protein-ligand complex. This chapter describes a protocol for conducting bottom-up, continuous uptake, proteolytic fragmentation HDX-MS experiments that can help identify and map the interacting peptides of a protein-ligand interface. This tutorial outlines the fundamental theory governing hydrogen exchange; provides practical information regarding the preparation of protein samples and solutions; and describes the exchange reaction, reaction quenching, enzymatic digestion, chromatographic separation, and peptide analysis by MS. Tables list representative combinations of fluidic components used by HDX-MS researchers and summarize the available HDX-MS analysis software packages. Additionally, two HDX-MS case studies are used to illustrate protein-ligand interactions involving: (1) a continuous sequence of interacting residues and (2) a set of discontinuously numbered residues, residing spatially near each other.

Keywords: Epitope; Higher order structure; Hydrogen-deuterium exchange; Mass spectrometry; Molecular dynamics; Protein structure; Protein–ligand interaction; Proteomics; Protocol.

MeSH terms

  • Deuterium / chemistry
  • Epitopes / chemistry*
  • Hydrogen / chemistry
  • Ligands
  • Mass Spectrometry / methods*
  • Molecular Dynamics Simulation
  • Peptides / analysis
  • Peptides / chemistry
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / metabolism
  • Proteolysis
  • Proteomics*


  • Epitopes
  • Ligands
  • Peptides
  • Proteins
  • Hydrogen
  • Deuterium