MEMHDX

MEMHDX analyzes Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) datasets to quantify and validate deuterium incorporation and protein dynamics, including applications to large protein complexes and membrane proteins from data produced by modern mass spectrometers and Ultra-High Performance Liquid Chromatography (UHPLC).

Key Features:

• Automated workflow: Automates processing of large HDX-MS datasets to generate peptide-level fitted models and global experimental summaries.
• Statistical validation: Implements a mixed-effects model per peptide across experimental conditions and time points, accounting for temporal dynamics and the number of independent replicates and modelling both fixed and random effects.
• P-value adjustments: Computes two adjusted P-values per peptide assessing the 'Change in dynamics' and the 'Magnitude of ΔD', used for classification via a 'Logit' representation.
• Visualization outputs: Produces plots of raw data and fitted models for each peptide, visualizations of calculated P-values, a global experimental view, and mappings of peptides onto amino acid sequences and 3D structures to display deuterium incorporation.

Scientific Applications:

• Large protein complex analysis: Quantifies deuterium uptake and dynamics in large multi-subunit assemblies using HDX-MS data.
• Membrane protein studies: Assesses deuterium incorporation and conformational dynamics of membrane proteins under different conditions.
• Protein dynamics and interactions: Detects and quantifies condition-dependent structural changes and interaction-induced dynamics at peptide resolution.

Methodology:

Automated processing of HDX-MS datasets combined with peptide-wise mixed-effects modeling (accounting for fixed and random effects) across conditions and time points; calculation of two adjusted P-values per peptide ('Change in dynamics' and 'Magnitude of ΔD') with classification via a 'Logit' representation; generation of plots, fitted peptide models, P-value visualizations, global summaries, and peptide-to-structure mappings.