HDX match software for the data analysis of top-down ECD-FTMS hydrogen/deuterium exchange experiments.

Hydrogen/deuterium exchange (HDX) combined with mass spectrometry is a powerful technique for studying protein structure. The recently developed top-down ECD-FTMS HDX approach (Pan J. et al., JACS, 2008) allows determination of the hydrogen/deuterium exchange of a protein's amide bonds, down to the single residue resolution. One of the existing limitations of this technology has been the laborious manual analysis of the MS/MS spectra. Here we present a software program for processing the data from these experiments. This program assigns the c- and z-fragment ion series of the protein, and calculates the number of the exchanged amide protons for each fragment by fitting the theoretically predicted isotopic envelopes of the deuterated fragments to the experimental data. Graphical Abstract ᅟ.