Metabolome Searcher

Metabolome Searcher identifies compounds in mass spectrometry (MS) output by leveraging genome-restricted metabolic capabilities to produce organism-specific candidate metabolite lists and associated putative pathways.

Key Features:

• Genome-restricted search: Uses an organism's genome as a dynamic database to restrict candidate metabolites to those the organism can produce.
• Input types: Accepts compound name, formula, SMILES structure, and mass as search inputs.
• Analytical parameter filtering: Applies user-specified mass deviation, adducts, and detection mode to refine tentative identifications.
• Batch processing: Supports multiple queries via text files generated manually or from MS analysis software.
• Output: Returns a genome-restricted list of possible compound identifications with associated putative metabolic pathways.
• Database linkage: Provides HTML output with hyperlinks to curated metabolic databases housed within ProCyc (a Pathway Tools platform) and the KEGG Pathway database.
• Extended identification scope: Enables candidate identifications beyond entries in empirical compound databases by integrating genome-encoded metabolic information.

Scientific Applications:

• Metabolite identification in MS data: Narrows candidate lists for MS-derived masses using organism-specific metabolic capability.
• Discovery of uncataloged metabolites: Extends possible identifications to metabolites not present in empirical compound databases.
• Microbial metabolism analysis: Supports investigation and interpretation of microbial metabolic pathways.
• Pathway-level interpretation: Links putative metabolites to metabolic pathways via ProCyc and KEGG for deeper biological interpretation.

Methodology:

Uses the organism genome as a database to filter MS-derived candidate compounds based on inputs (compound name, formula, SMILES, mass), applies mass deviation, adduct, and detection mode parameters, accepts batch text-file queries, and outputs a genome-restricted candidate list with putative metabolic pathways and hyperlinks to ProCyc (a Pathway Tools platform) and the KEGG Pathway database.