Graph-DOM

Graph-DOM analyzes ultra-high-resolution Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (ESI-FT-ICR MS/MS) data acquired using Data Independent Fragmentation to compute ordered fragmentation pathways and identify structurally related dissolved organic matter (DOM) compounds in aquatic ecosystems.

Key Features:

• Data compatibility: Processes MS/MS data acquired by Data Independent Fragmentation using ESI-FT-ICR MS/MS.
• Ultra-high-resolution spectrum processing: Parses and interprets compiled output files from hundreds of fragment spectra.
• Graph-theoretic pathway computation: Employs graph algorithms to compute ordered fragmentation pathways.
• Scale of computations: Computes over half a million ordered fragmentation pathways for 764 isolated precursor ions.
• Neutral-loss modeling: Considers up to seven vector segments categorized as neutral losses: CH2, CH3, O, CH4, H2O, CO, and CO2.
• Family identification via overlap analysis: Identifies families of structurally related molecules through analysis of pathway overlaps.
• Output for network visualization: Generates output files compatible with network visualization software such as Cytoscape.
• Adjustable parameters and low-abundance support: Provides configurable overlap-length parameters and configurations for low-abundance compounds containing CHOS, CHON, and CHONS.
• Performance: Processes computed fragmentation pathways typically within minutes.

Scientific Applications:

• DOM structural characterization: Enables molecular-level characterization of dissolved organic matter in aquatic ecosystems.
• Detection of structurally related compounds: Reveals molecular families and structural relationships within complex DOM mixtures.
• Analysis of heteroatom-bearing low-abundance species: Supports analysis of low-abundance compounds containing CHOS, CHON, and CHONS.
• Network-based interpretation: Facilitates network visualization and interpretation of fragmentation-derived relationships.

Methodology:

Processes compiled ESI-FT-ICR MS/MS Data Independent Fragmentation output, applies a graph-theoretic approach to compute ordered fragmentation pathways (over 500,000 pathways for 764 precursor ions), models up to seven neutral-loss vector segments (CH2, CH3, O, CH4, H2O, CO, CO2), analyzes pathway overlaps to identify molecular families, and exports Cytoscape-compatible network files.