DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data

The open-source software, DECA, provides comprehensive back-end analysis of HDX-MS data that addresses the recent recommendations for HDX-MS data analysis and presentation. It provides options for back-exchange correction and rigorous statistical analysis of the significance of differences in exchange. [Display omitted] Highlights •Open source software for comprehensive HDX-MS data analysis.•Automatic back-exchange correction options.•Rigorous statistical analysis of the significance of uptake differences.•High quality visualization tools. Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) has become widely popular for mapping protein-ligand interfaces, for understanding protein-protein interactions, and for discovering dynamic allostery. Several platforms are now available which provide large data sets of amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data. Although many of these platforms provide some down-stream processing, a comprehensive software that provides the most commonly used down-stream processing tools such as automatic back-exchange correction options, analysis of overlapping peptides, calculations of relative deuterium uptake into regions of the protein after such corrections, rigorous statistical analysis of the significance of uptake differences, and generation of high quality figures for data presentation is not yet available. Here we describe the Deuterium Exchange Correction and Analysis (DECA) software package, which provides all these downstream processing options for data from the most popular mass spectrometry platforms. The major functions of the software are demonstrated on sample data.