Sierra Analytics is pleased to present HDExaminer, a complete software solution for bottom-up H-D Exchange MS data analysis.

HDExaminer provides powerful functionality to give a comprehensive picture of the deuteration uptake behavior of a protein. This information can be used to help determine protein folding behavior, protein-drug interactions, and other useful results.


  • Imports MS data from many different vendor formats
  • Supports replicate experiments seamlessly, providing comparison functionality and significance analysis
  • Imports peptide search results from SEQUEST HTML, Mascot XML, Proteome Discoverer .xls, pepXML, or generic tabular data, allowing compatibility with many peptide search packages
  • Allows export of all calculated results in graphical or tabular formats
  • Can export data suitable for import into PyMOL
  • Works with both low-resolution and high-resolution MS data
  • Sophisticated matching algorithm finds peptide isotope clusters even with noisy data or overlapping peptides

    Overlapping Peptides

  • Assigns a confidence level to each peptide isotope cluster match, saving valuable time during manual verification of results

  • Includes comprehensive data visualization tools, including uptake plots and heat maps, allowing you to quickly locate potential trouble spots in your data before they impact your results
  • Allows you to easily compare protein states (for example, ligand-bound vs unbound, modified vs unmodified, mutant vs wild type)
    Difference Heat Map

HDExaminer is the product of Sierra's years of experience writing H-D Exchange software tools. Please see our publication history with leading researchers in the field.  The result of this extensive experience is a high-quality, easy-to-use software application which is the most widely-useful, vendor-neutral solution available on the market.

A fully-functional 30-day trial version is available upon request.  Please contact sales@MassSpec.com for more information.