# HaDeX2: multi-dimensional analysis of hydrogen–deuterium exchange mass spectrometry data

## TL;DR

HaDeX2 is a new tool for analyzing complex HDX-MS data across multiple dimensions to gain biological insights.

## Contribution

HaDeX2 introduces a multi-dimensional analysis framework for HDX-MS data with statistical inferences and visualizations.

## Key findings

- HaDeX2 enables analysis across five dimensions: sequence, time, biological states, peptide charge, and replicates.
- The tool is available as an R package and web server with a dedicated GUI companion.
- It provides statistical inferences and visualizations to interpret HDX-MS data.

## Abstract

Hydrogen–Deuterium Exchange Mass Spectrometry (HDX-MS) monitors deuterium uptake at the peptide level, in a time-dependent manner. It produces complex, multi-dimensional data that must be interpreted at minimum both the temporal and sequence levels. Specialized tools are therefore essential to preprocess, integrate, and analyze HDX-MS data and translate it into meaningful biological insights. HaDeX2 provides statistical inferences and their visualizations across five dimensions of HDX-MS data: protein sequence, time, biological states, peptide charge and experimental replicates.

HaDeX2 is freely available as an R package (https://github.com/hadexversum/HaDeX2; https://doi.org/10.5281/zenodo.18543703) and web server (https://hadex2.mslab-ibb.pl/). To run the GUI locally, users should install a dedicated companion package (https://github.com/hadexversum/HaDeXGUI).