HDExaminer takes your MS data calculates the deuteration level at each residue that most closely matches the results of your measured peptides. This allows you to quickly assess which residues are the most important ones for further study.

If your experiment involves comparing two protein states, such as ligand-bound vs. unbound, mutant vs. wild type or modified vs. unmodified, HDExaminer allows you to combine the data from each experiment to show you exactly what the difference is between any two of your states.

Ease of use is a fundamental goal of HDExaminer’s interface. You can browse to any individual result, view its isotope cluster and extracted ion chromatogram, and adjust calculation ranges, if necessary. The color-coded table shows whether a result is high-, medium- or low-confidence. Confidence levels are assigned automatically based on how well the actual and theoretical isotope clusters match for the result, and may be changed by the user.

In the Peptides View, you can look at uptake plots for each of your measured peptides. Error bars tell you how your replicates impact the statistical significance of the differences you see. As above, color coding tells you the confidence level of each peptide.

The peptide plot allows you to see changes in deuteration on a per-peptide basis, either as a residual plot or a butterfly plot.