HRaDeX

HRaDeX computes high-resolution deuterium uptake rates from HDX-MS data, enabling accurate reconstitution of experimental normalized deuterium uptake curves at the amino acid level by analyzing deuterium uptake trajectories of superimposed peptides.

Key Features:

• High-resolution kinetic parameter estimation: Provides deuterium uptake kinetic parameters at amino acid resolution by considering deuterium uptake trajectories of superimposed peptides rather than peptide fragment averages.
• Single-state and comparative HDX-MS support: Processes data from both single-state and comparative HDX-MS studies.
• Dual implementation: Available as both an R package and a web server.
• Benchmarked accuracy: Achieves an average root-mean-square error of 7.15% in reconstitution of experimental normalized deuterium uptake curves across eight benchmark data sets.

Scientific Applications:

• Protein dynamics and stability analysis: Captures local and global unfolding events in protein structures through hydrogen-deuterium exchange monitored by mass spectrometry (HDX-MS).
• Region-specific structural characterization: Overcomes the limitation of proteolytic digestion in HDX-MS, which breaks proteins into peptide fragments and causes HDX data to reflect averages rather than individual amino acid information.
• Comparative HDX-MS studies: Enables comparison of protein states to identify differential dynamics and stability.

Methodology:

HRaDeX uses a computational algorithm that analyzes deuterium uptake trajectories of superimposed peptides to compute high-resolution deuterium uptake kinetic parameters.