HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX-MS Data

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is crucial for studying protein dynamics and stability.
• Current HDX-MS methods require proteolytic digestion, leading to averaged data over peptide fragments, limiting residue-level insights.
• This averaging obscures detailed information about local protein unfolding events.

Purpose of the Study:

• To introduce a novel computational method, HRaDeX, for high-resolution deuterium uptake kinetic parameter determination.
• To overcome the limitations of peptide averaging in conventional HDX-MS analysis.
• To provide a tool for analyzing superimposed peptide deuterium uptake trajectories for enhanced protein structure insights.

Main Methods:

• Development of the HRaDeX computational algorithm.
• Processing of deuterium uptake trajectories from superimposed peptides.
• Validation using eight benchmark HDX-MS data sets, covering single-state and comparative studies.
• Implementation as a user-friendly web server and an R package.

Main Results:

• HRaDeX provides high-resolution deuterium uptake kinetic parameters.
• The method successfully analyzes superimposed peptide data for improved accuracy.
• Benchmark data analysis showed an average root-mean-square error of 7.15% in reconstituting experimental deuterium uptake curves.
• The algorithm demonstrates robust performance across diverse HDX-MS datasets.

Conclusions:

• HRaDeX significantly enhances the resolution and accuracy of HDX-MS data analysis.
• The computational approach effectively addresses the limitations of proteolytic digestion and peptide averaging.
• HRaDeX offers a valuable tool for detailed investigation of protein dynamics and stability at a near-residue level.