---
title: "Annotate Metabolome"
description: "Annotate Metabolome: an omics recipe chaining metabolomics, metabolomics."
tags:
  - recipes
  - omics
tools:
  - metabolomics
  - metabolomics
generated: true
source: quickActionConfig:metabolomics-annotate-pathway
---

> **Generated recipe**

> Seeded from a curated quick-action prompt. The prompt below runs the real
> routing — copy it, change the target, and run.

> **Recommended pairing**

> These tools are commonly run together — they cover complementary ground on the same input.

**Best fit:** annotate metabolome — an omics goal.

**Try this prompt** — [open in a guest chat](/chat/new?guest=true&prompt=Search%20HMDB%20for%20all%20tryptophan-kynurenine%20pathway%20metabolites%20(tryptophan%2C%20kynurenine%2C%20kynurenic%20acid%2C%20quinolinic%20acid%2C%203-HAA%2C%20picolinic%20acid)%2C%20retrieve%20their%20exact%20masses%20and%20MS%2FMS%20spectra%2C%20map%20to%20KEGG%20pathway%20hsa00380%2C%20cross-reference%20with%20MetaCyc%20for%20bacterial%20vs%20human%20pathway%20steps%2C%20and%20recommend%20whether%20the%20kynurenine%2Ftryptophan%20ratio%20or%20a%20specific%20kynurenine%20metabolite%20is%20the%20most%20robust%20immunotherapy%20response%20biomarker%20for%20a%20prospective%20correlative%20study%3F).

> 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?

_A real `metabolomics-annotate-pathway` quick-action prompt — open it in a guest chat, then swap in your own compound or target._

## The prompt

```text
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](/docs/metabolomics) — Compound identification via exact mass, MS/MS spectral matching (HMDB, MoNA), and isotope pattern scoring
- [metabolomics](/docs/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?](/docs/which-tool) — match a single goal to a tool.
- [Workflows](/docs/workflows) — every workflow and recipe.
- [How the orchestrator picks tools](/docs/how-orchestration-works) — the same chain from a plain-language goal.