HDgraphiX: A web-based tool for visualization of hydrogen deuterium exchange mass spectrometry data

Abstract

SummaryHydrogen deuterium exchange mass spectrometry (HDX-MS) investigates protein structural changes by measuring deuterium incorporation into the protein amide backbone. Due to richness of information provided on protein conformational dynamics, HDX-MS data can be challenging to visualize effectively. To address this, we have developed HDgraphiX, a web-based tool that visualizes HDX data by processing outputs from two popular analysis software packages, DynamX (Waters Corp.) and HDExaminer (Sierra Analytics Inc). HDgraphiX performs statistical analyses, filters data based on statistical significance and presents the results in several forms of user-friendly publication-quality heatmaps (Chiclet plots). Unique features of this tool include the generation of Woods plots, volcano plots, and PyMOL colouring scripts, which are used to map deuterium uptake differences onto protein structures. Additionally, HDgraphiX offers numerous advanced options for customizing data processing and plotting without the need for manual data editing. Availability and ImplementationHDgraphiX is available free of charge for all users at https://hdgraphix.net, the Python script and HTML template are deposited at https://github.com/KentV-UofG/HDgraphiX.