PepFoot

PepFoot processes mass spectrometry (MS) data from protein footprinting experiments to quantify peptide-level fractional modification (f_m) and visualize differential labeling for mapping protein surface accessibility and binding sites.

Key Features:

• .mz5 compatibility: Supports the open-source .mz5 file format for compatibility with MS data from major instrument manufacturers.
• Semi-automated batch analysis: Performs semi-automated batch processing to determine the degree of fractional modification (f_m) of peptides across experiments.
• Scalable processing: Automates analysis across batches to increase throughput for large volumes of MS data generated by covalent footprinting techniques.
• Histogram plotting and structure mapping: Generates histogram plots of f_m for each peptide and maps differential labeling patterns onto imported protein structures.
• Labeling-chemistry validation: Validated with carbene and hydroxyl radical labeling experiments.

Scientific Applications:

• Protein surface accessibility mapping: Quantifies peptide-level labeling to identify solvent-accessible regions on proteins.
• Binding-site identification: Visualizes differential labeling to localize ligand or partner binding sites on protein structures.
• Structural biology and biochemistry studies: Supports analysis of protein conformational changes and interaction dynamics from footprinting MS data.
• Drug discovery and enzyme design: Provides peptide-resolved labeling data to inform target engagement and engineering of protein interfaces.
• Protein–protein interaction analysis: Enables detection of interaction-induced changes in labeling patterns across peptides.

Methodology:

Workflow uses an initial user-guided interrogation of one data file to set parameters, followed by automated batch processing to determine peptide-level fractional modification (f_m).