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Metabolite annotation and identification

CMMC-KB

A community-curated knowledgebase for microbial metabolites that links reference MS/MS evidence, microbial producers, annotations, and GNPS2 analysis resources.

LC-MSUntargeted metabolomicsMetabolite profilingWeb applicationFree web service
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Overview

CMMC-KB is part of the Collaborative Microbial Metabolite Center infrastructure for community curation of microbial small molecules. It is designed to consolidate evidence connecting microbial metabolites with spectra, structures, producers, and contextual metadata, and to make that knowledge reusable in GNPS2 analyses such as molecular-network enrichment and microbial contextualization. The associated scientific description is currently a 2026 preprint.

What can this tool do?

Spectral-library matchingMetadata-based contextualizationProvenance tracking

Common uses

  • Curate and retrieve microbial-metabolite knowledge linking spectra, chemical annotations, and producer context.
  • Enrich GNPS2 analyses with community-curated microbial metabolite evidence.
  • Support community deposition and validation of microbial metabolite annotations.
  • Download curated spectra and metadata for reuse while keeping their supporting evidence attached.

Scientific fit

Primary function

Metabolite annotation and identification

Other functions

Reference data and database search, Data management and sharing

Analysis types

Untargeted metabolomics, Metabolite profiling

MS level

MS/MS

Acquisition

Data-dependent acquisition (DDA), Targeted MS/MS, General or unspecified acquisition

Ion mobility

Ion mobility not required

Data compatibility

Inputs

Mass spectra, Molecular structures, Sample metadata

Outputs

Mass spectra, Compound list or annotations, Sample metadata, Human-readable report

Input formats

MGF, SMILES or InChI, CSV or TSV, Spectrum identifiers and curated compound metadata

Output formats

CSV or TSV, MGF

Scope and considerations

Designed for

  • Community knowledge curation and downstream interpretation of microbial metabolomics data.

Not designed for

  • Treating every curated occurrence or source annotation as experimentally proven microbial biosynthesis.

Important requirements

  • Curated metabolite/spectral evidence for deposition or GNPS2-compatible analysis results for downstream use.

Considerations

  • The main scientific description is currently a preprint and the knowledgebase is actively expanding.
  • Curated evidence can span different levels of structural and biological confidence; users should inspect supporting evidence for individual annotations.
  • Inspect the evidence and source category for each entry; host, food, drug and exposure-related molecules can also be represented.

Access and documentation

Primary accessDocumentation

Hosted access and any account or usage requirements should be checked at the linked service. Access to a web service does not establish the license of its code or reference data.

Evidence and review

Documentation-based editorial pass on 6 September 2026: scope, interpretation limits and practical use reviewed against the linked official documentation and cited literature. Software execution, service availability and developer verification were not assessed.

Core publications

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

  1. Preprint · not peer reviewed Mannochio-Russo H, Goncalves Nunes WD, Xing S, et al. Community Curation of Microbial Metabolites Enables Biological Insights of Metabolomics Data. bioRxiv (2026). Preprint; not peer reviewed. doi:10.64898/2026.01.24.701521

Related tools

microbeMASSTComplementary to · A taxonomically informed GNPS search service that connects query MS/MS spectra to matching spectra from curated bacterial, fungal, and archaeal monoculture datasets.GNPSPart of · A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.CMMC DashboardIntegrates with · Visualize CMMC enrichment results alongside feature abundances, metadata and molecular-network information.MetaboAppsIntegrates with · A modular collection of browser-based downstream analysis applications that extend GNPS2 results with targeted interpretation, statistics, metadata, and domain-specific readouts.

Entry history

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

  1. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  2. 2026-09-07 · Entry update

    Expand and document 31 metabolomics tools and resources

    View change · Entry at this revision
  3. 2026-08-24 · First committed entry

    Complete GNPS SIRIUS and MZmine tool ecosystems

    View change · Entry at this revision

Full GitHub history