Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Metabolite annotation and identification

khipu

Group LC-MS isotope and adduct features into empirical compounds and infer neutral masses.

LC-MSPython packageCommand lineOpen source
Access toolSuggest an update

Overview

khipu provides Python and command-line pre-annotation of feature tables. Its graph/tree representation links related ions; the associated Khipu-web publication extends access for stable-isotope tracing. These groupings do not by themselves establish molecular identity.

What can this tool do?

Adduct and isotope grouping

Common uses

  • Reduce redundant isotope/adduct features before downstream interpretation.

Scientific fit

Primary function

Metabolite annotation and identification

Data compatibility

Inputs

Feature or peak table

Outputs

Compound list or annotations

Input formats

Tab-delimited feature ID, m/z, retention time and sample intensity columns

Output formats

Empirical-compound annotations in JSON and TSV

Scope and considerations

Designed for

  • LC-MS ion grouping, including configured isotope-tracing patterns.

Not designed for

  • Confirmed structural identification or a metabolic-flux solver.

Important requirements

  • A preprocessed feature table and appropriate ion-mode, mass and retention-time tolerances.

Considerations

  • Grouping depends on expected ion patterns and preprocessing quality.

Access and documentation

Primary access

Python package; the repository also links a web interface. Check that interface separately for hosted availability.

License: BSD-3-Clause

Evidence and review

Discovered through the Enveda review intake; official repository and primary publication metadata checked on 2026-10-02. Editorial review only; software and performance not execution-tested.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Generalized Tree Structure to Annotate Untargeted Metabolomics and Stable Isotope Tracing Data. Analytical Chemistry (2023). doi:10.1021/acs.analchem.2c05810
  2. Annotation of Metabolites in Stable Isotope Tracing Untargeted Metabolomics via Khipu-web. Journal of the American Society for Mass Spectrometry (2024). doi:10.1021/jasms.4c00175

Related tools

asariIntegrates with · asari uses khipu for pre-annotation.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-02 · First committed entry

    Add five source-verified isotope and spatial tools from Enveda intake

    View change · Entry at this revision

Full GitHub history