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

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is crucial for studying protein structural dynamics.
• Analyzing and visualizing the rich information from HDX-MS experiments presents significant challenges.
• Existing software outputs require effective integration and presentation methods.

Purpose of the Study:

• To develop a user-friendly web-based tool, HDgraphiX, for visualizing HDX-MS data.
• To streamline the processing and statistical analysis of HDX-MS data from various software.
• To generate publication-quality visualizations and structural mapping of deuterium uptake.

Main Methods:

• HDgraphiX processes data outputs from DynamX, HDExaminer, and HDX Workbench.
• It performs statistical filtering and generates diverse plots like heatmaps, Woods plots, and volcano plots.
• The tool creates PyMOL and ChimeraX scripts for mapping data onto protein structures.

Main Results:

• HDgraphiX provides intuitive, publication-ready visualizations of HDX-MS data.
• It integrates statistical analysis and data filtering for significance assessment.
• Advanced customization options and session saving enhance usability and reproducibility.

Conclusions:

• HDgraphiX effectively addresses the visualization challenges of HDX-MS data.
• The tool enhances the interpretation of protein conformational dynamics.
• It serves as a valuable resource for researchers in structural biology and related fields.