Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Processing, analysis and visualization of Hydrogen Deuterium eXchange monitored by Mass Spectrometry experiments (HDX-MS). 'HaDeX2' introduces a new standardized and reproducible workflow for the analysis of the HDX-MS data, including uncertainty propagation, data aggregation and visualization on 3D structure. Additionally, it covers data exploration, quality control and generation of publication-quality figures. All functionalities are also available in the accompanying 'shiny' app.

HaDeX: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) is a staple technology in structural proteomics. HaDeX provides a analytic workflow for HDX-MS data available both as web server or R package, accompanied by dedicated application HaDeXGUI. This is a second version on previously published HaDeX.

Local instance of HaDeX package

You can install the latest development version of the package:

devtools::install_github("hadexversum/HaDeX2")

After installation GUI can be accessed locally:

library(HaDeX2)
HaDeX_GUI()

To run the GUI, the dedicated package HaDeXGUI is needed. If is not installed, the called function will check and inform if installation is needed.

Online manual

The HaDeX documentation is available online.

Funding

This work is supported by Foundation of Polish Science (TEAM TECH CORE FACILITY/2016-2/2 Mass Spectrometry of Biopharmaceuticals - improved methodologies for qualitative, quantitative and structural characterization of drugs, proteinaceous drug targets and diagnostic molecules), Narodowe Centrum Nauki (Preludium Bis 1 2019/35/O/NZ2/03745 Wysokorozdzielcza analiza danych z eksperymentów wymiany proton-deuter monitorowanych spektrometrią mas) as well as (Sonata 19 2023/51/D/NZ7/02847 Ujarzmić agregację z AmyloGraphem 2.0: baza danych i model predykcyjny modulatorów samoorganizacji amyloidowej), and Narodowa Agencja Wymiany Akademickiej (PPN/STA/2021/1/00025).