ExMS2

ExMS2 analyzes hydrogen-deuterium exchange mass spectrometry (HDX MS) data to identify and quantify peptide isotopic envelopes and extract residue-level hydrogen-deuterium exchange information for probing protein structure and dynamics.

Key Features:

• Integration with ExMS and HDsite: Incorporates enhanced functionalities from ExMS and residue-level analysis capability from HDsite for combined workflows.
• Peptide isotopic envelope analysis: Identifies and analyzes peptide isotopic envelopes within raw HDX MS data.
• Partially deuterated peptide identification and validation: Detects and validates numerous partially deuterated peptides to quantify deuterium uptake.
• Residue-level resolution: Extends peptide-level HDX information to residue-level mapping for site-specific exchange analysis.
• ETD, ECD and multimodal spectra modules: Provides modules for electron transfer dissociation (ETD), electron capture dissociation (ECD), and multimodal mass spectra analysis.
• Visualization of complex datasets: Generates presentation-oriented outputs to facilitate visualization and interpretation of HDX MS results.

Scientific Applications:

• Fine-scale epitope mapping: Enables high-resolution mapping of epitope regions through residue-level HDX measurements.
• Protein folding studies: Supports characterization of folding pathways and conformational dynamics via deuterium uptake patterns.
• Structure and structural-change analysis of large protein complexes: Facilitates investigation of structural organization and conformational changes in large complexes.
• Comprehensive proteomic HDX MS studies: Applies to broad proteomic analyses using multimodal and dissociation-based mass spectrometry data.

Methodology:

Computational methods explicitly include identification and analysis of peptide isotopic envelopes in raw HDX MS data, detection and validation of partially deuterated peptides, extension to residue-level mapping, and dedicated modules for ETD, ECD, and multimodal mass spectra analysis.