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

"This is the best analysis software I have used thus far."
-Laura Busenlehner, University of Alabama

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

Screenshot of Heat Map

  • Allows you to easily compare protein states (for example, ligand-bound vs unbound, modified vs unmodified, mutant vs wild type)

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.