coADAPTr

coADAPTr quantifies the extent of protein modification in covalent labeling mass spectrometry experiments, particularly hydroxyl radical protein footprinting (HRPF), enabling proteome-wide analysis of protein interaction sites and conformational changes.

Key Features:

• Duplicate Data Removal: Filters remove any duplicate data to improve fidelity.
• Arithmetic Mean Quantitation: Uses the arithmetic mean rather than the geometric mean for quantitation of the extent of modification.
• Enhanced Graphical Interpretations: Provides proteome-wide insights with enhanced graphical interpretations.
• High-Throughput Processing: Processes data up to 200 times faster than conventional methods such as Excel's Power Pivot.

Scientific Applications:

• Protein Interaction Site Mapping: Quantifies the extent of modification of proteins in multiple states (i.e., ligand free vs ligand-bound) to provide information on protein interaction sites.
• Conformational Change Analysis: Identifies regions of conformational change in proteins through differential modification analysis.
• Structural Proteomics: Supports proteome-wide data analysis for deciphering complex structural biology data via HRPF and other covalent labeling MS methods.

Methodology:

coADAPTr mimics the functions used in previous quantitation platforms using PowerPivot in Microsoft Excel but with fewer steps, implementing filters for duplicate data removal and arithmetic mean calculation for quantitation of the extent of modification.