Protein dynamics with HDX-MS
Turning hydrogen–deuterium exchange measurements into interpretable views of protein behaviour.
Proteins in motion
Protein function depends on more than a single structure. Hydrogen–deuterium exchange mass spectrometry, or HDX-MS, measures changes in deuterium uptake over time and helps researchers investigate protein dynamics and differences between experimental states.
The resulting data have several dimensions: sequence position, exchange time, biological state, peptide charge and replicates. Analysing them together requires careful aggregation, quality control and an explicit treatment of uncertainty.
Questions we explore
- How can complex measurements be summarised without losing their experimental context?
- Which differences between protein states are supported by the data and their uncertainty?
- What additional information can overlapping peptides provide about local protein dynamics?
Our approach
We develop tools that connect statistical analysis with visual exploration. HaDeX2 supports multidimensional analysis and visualisation of HDX-MS data, helping researchers examine coverage, measurement variability and differences between experimental conditions.
Our high-resolution work addresses the relationship between peptide measurements and more local estimates of deuterium uptake. HRaDeX explores residue-level uptake rates through kinetic modelling. These approaches provide complementary ways to interrogate the data, with the underlying assumptions remaining important to interpretation.
Tools, projects & people
Explore HaDeX and HRaDeX in the software catalogue, and read Weronika Puchała’s academic CV.
Publications & research stories
HaDeX2: exploring the full experiment
Statistical analysis and visualisation across the dimensions of HDX-MS data.
HRaDeX: a higher-resolution view
Reconstructing deuterium uptake rates from peptide-level measurements.