HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry

J Am Soc Mass Spectrom. 2012 Feb;23(2):425-9. doi: 10.1007/s13361-011-0234-5. Epub 2011 Nov 15.


Hydrogen/deuterium exchange in combination with mass spectrometry (H/D MS) is a sensitive technique for detection of changes in protein conformation and dynamics. However, wide application of H/D MS has been hindered, in part, by the lack of computational tools necessary for efficient analysis of the large data sets associated with this technique. We report a novel web-based application for automatic analysis of H/D MS experimental data. This application relies on the high resolution of mass spectrometers to extract all isotopic envelopes before correlating these envelopes with individual peptides. Although a fully automatic analysis is possible, a variety of graphical tools are included to aid in the verification of correlations and rankings of the isotopic peptide envelopes. As a demonstration, the rate constants for H/D exchange of peptides from rabbit muscle pyruvate kinase are mapped onto the structure of this protein.

Publication types

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

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Databases, Protein
  • Deuterium Exchange Measurement / methods*
  • Internet
  • Mass Spectrometry / methods*
  • Models, Molecular
  • Peptides / chemistry*
  • Peptides / metabolism
  • Pyruvate Kinase / chemistry
  • Pyruvate Kinase / metabolism
  • Rabbits
  • Software*
  • Spectroscopy, Fourier Transform Infrared


  • Peptides
  • Pyruvate Kinase