ExMS

ExMS analyzes hydrogen-deuterium exchange-mass spectrometry (HDX-MS) data in MATLAB to identify and characterize peptide isotopic peaks and envelopes for probing protein structural dynamics.

Key Features:

• MATLAB implementation: Implemented as a MATLAB program for processing HDX-MS datasets.
• Processing of crowded mass spectra: Automatically identifies and characterizes overlapping peptide fragments from high-resolution mass spectrometry data, enabling analysis of hundreds of sequentially overlapping peptides.
• Automated isotopic identification: Scans MS data to locate individual isotopic peaks and envelopes associated with a predefined list of peptides identified by MS/MS.
• Overlap-tolerant identification tests: Applies multiple tests to ensure accurate peptide identification in the presence of chromatographic and mass-spectrometric overlaps.
• Multi-modal envelope handling: Detects and manages multi-modal isotopic envelopes arising from static or dynamic structural heterogeneity and EX1 exchange behavior.
• Time-point processing: Processes multiple sequential HDX time points autonomously, with reported throughput of ~2 seconds per peptide per time point on a standard desktop computer.
• Manual verification support: Provides rapid manual checking and decision-making capabilities when ambiguity arises in identifications.
• Reporting and parameter adjustment: Includes subroutines that generate stepwise performance reports at each test stage to facilitate parameter adjustment.
• Isotopic envelope deconvolution and plotting: Deconvolutes isotopic envelopes and plots time courses of single- and multi-modal hydrogen-deuterium exchange processes.

Scientific Applications:

• Protein folding and dynamics: Enables analysis of protein folding, conformational changes, and structural heterogeneity via HDX-MS-derived peptide exchange patterns.
• Protein interactions: Facilitates characterization of protein–ligand and protein–protein interaction sites through localized HDX-MS measurements.
• Structural biology and proteomics: Supports structural biology and proteomics studies that require high-resolution mapping of backbone amide solvent accessibility and dynamics.

Methodology:

Uses high-resolution MS data and a predefined peptide list from MS/MS to perform automated scans for isotopic peaks and envelopes, applies a series of tests to validate identifications in the presence of overlapping signals or structural heterogeneity, deconvolutes isotopic envelopes, and plots HDX time courses for sequential time points.