# HydroBot: Software for Interactive Hydrogen/Deuterium-Exchange Mass Spectrometry Multistate Analysis

## TL;DR

HydroBot is a new software tool for analyzing hydrogen/deuterium-exchange mass spectrometry data, enabling interactive and comprehensive insights into protein dynamics and interactions.

## Contribution

HydroBot introduces interactive and automated tools for multistate and nonequilibrium HDX-MS data analysis and visualization.

## Key findings

- HydroBot supports automated uptake plotting and statistical testing of differences between protein states.
- The software includes interactive visualization modes like bar plots, Woods plots, and heatmaps.
- Clustering methods reveal correlated structural dynamics in multistate HDX data.

## Abstract

Hydrogen/deuterium-exchange
mass spectrometry (HDX-MS) is a powerful
technique for probing protein dynamics, stability, and interactions.
However, multistate and nonequilibrium experiments currently do not
have available analysis tools. We present HydroBot, a software designed
for comprehensive and interactive HDX-MS data analysis and visualization.
HydroBot supports rapid and automated uptake plotting, statistical
testing of differences between protein states, and multiple interactive
visualization modes including bar plots, Woods plots, and heatmaps.
Statistical tools such as volcano plots and error distribution analyses
are integrated to assess data robustness, enabling interactive exploration
of labeling differences. Correlated structural dynamics are revealed
by k-means or hierarchical clustering, facilitating
pattern discovery within multistate HDX data for proteins at equilibrium
and nonequilibrium. Additionally, scripts are created to enable visualization
of HydroBot analyses on protein structures. This user-friendly tool
streamlines HDX-MS validation and interpretation from processed data
to biologically relevant insights.