reactomics

reactomics leverages high-resolution paired mass distance (PMD) analysis of mass spectrometry data to detect and analyze chemical reactions among small molecules in untargeted metabolomics.

Key Features:

• High-resolution PMD analysis: Calculates paired mass distances (PMDs) from high-resolution mass spectrometry to reveal mass differences corresponding to biochemical transformations.
• PMD Network Analysis: Constructs and examines networks based on PMD-derived relationships to reveal interactions among small molecules.
• Reaction annotation via database mining: Links PMDs to known biochemical reactions by mining small molecule and reaction databases.
• Source appointment of unknown compounds: Associates unknown compounds with potential biochemical sources or origins through PMD–reaction associations.
• Biomarker reaction discovery: Identifies reaction-based biomarkers complementary to compound-centric metabolomics approaches.
• R implementation (pmd package): Implements the analytical framework and provides access to reaction/PMD databases via the pmd R package.

Scientific Applications:

• Environmental studies: Investigates biological fate and environmental impact of small molecules through reaction-level analysis.
• Physiological response investigations: Examines metabolic responses and biochemical transformations underlying physiological perturbations.
• Reaction-centric untargeted metabolomics: Retrieves biochemical relationships from untargeted data without prior compound identification.
• Dynamic metabolite interaction studies: Explores interactions among metabolites in complex biological systems.

Methodology:

Computationally, reactomics calculates PMDs from mass spectrometry data and links those PMDs to known biochemical reactions by mining small molecule and reaction databases; the approach is implemented in R via the pmd package, which provides the analytical framework and reaction/PMD databases.