Annotate Metabolome

Best fit: annotate metabolome — an omics goal.

The prompt

Search HMDB for all tryptophan-kynurenine pathway metabolites (tryptophan, kynurenine, kynurenic acid, quinolinic acid, 3-HAA, picolinic acid), retrieve their exact masses and MS/MS spectra, map to KEGG pathway hsa00380, cross-reference with MetaCyc for bacterial vs human pathway steps, and recommend whether the kynurenine/tryptophan ratio or a specific kynurenine metabolite is the most robust immunotherapy response biomarker for a prospective correlative study?

What each tool contributes

• metabolomics — Compound identification via exact mass, MS/MS spectral matching (HMDB, MoNA), and isotope pattern scoring
• metabolomics — Metabolic pathway enrichment analysis (KEGG, SMPDB) with topology-aware scoring and metabolic flux context

Why these tools pair

Metabolite annotation identifies compounds from MS/MS spectra via HMDB and spectral library matching while pathway mapping places identified metabolites onto KEGG/Reactome metabolic networks — annotation alone provides a compound list, but pathway mapping reveals which metabolic circuits are perturbed, enabling mechanistic interpretation of drug metabolism effects and disease-associated metabolic reprogramming

Data flow

Every tool operates on the same input: metabolite_name.

Read next

• Which tool? — match a single goal to a tool.
• Workflows — every workflow and recipe.
• How the orchestrator picks tools — the same chain from a plain-language goal.