HDgraphiX: A Web-Based Tool for Visualization of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Abstract

Hydrogen−deuterium exchange mass spectrometry (HDX-MS) investigates protein structural changes by measuring deuterium incorporation into the protein amide backbone. Due to the 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-MS data by processing outputs from several popular analysis software packages including DynamX, HDExaminer, and HDX Workbench. HDgraphiX performs statistical analyses, filters data based on statistical significance, and presents the results as user-friendly publication-quality visualizations, including heatmaps (Chiclet plots), Woods plots, ladder plots, and volcano plots. Users can optionally generate PyMOL and ChimeraX coloring scripts 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. To improve usability, users have the option to download a file containing all input settings, which can be reuploaded alongside HDX-MS data to avoid manual re-entry of custom settings.