Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Molecular networking and chemical similarity

SGMNS

SGMNS propagates candidate metabolite annotations through a structure-guided background molecular network.

LC-MSUntargeted metabolomicsCommand lineSource available with restrictions
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Overview

SGMNS propagates candidate metabolite annotations through a structure-guided background molecular network. Its documented workflow combines processed LC-HRMS features, tandem spectra and known seed metabolites with a default or custom structure database.

What can this tool do?

Structure-database searching

Common uses

  • SGMNS propagates candidate metabolite annotations through a structure-guided background molecular network.

Scientific fit

Primary function

Molecular networking and chemical similarity

Other functions

Metabolite annotation and identification

Analysis types

Untargeted metabolomics

Data compatibility

Inputs

Feature or peak table, Mass spectra

Outputs

Compound list or annotations, Statistical results

Input formats

Calibrated peak CSV, MGF spectra, seed lists and background database

Output formats

Network-propagated candidate metabolite annotations

Scope and considerations

Designed for

  • SGMNS propagates candidate metabolite annotations through a structure-guided background molecular network.

Not designed for

  • Raw peak picking or structure confirmation independent of seed accuracy and background-network coverage.

Important requirements

  • Prepared positive/negative-mode peak CSV tables, MGF spectra, seed-metabolite lists and a configured background network; retention times must be calibrated to the background conditions.

Considerations

  • Ion redundancy removal and retention-time calibration are upstream prerequisites. The default network and imported seed errors can propagate through subsequent annotations.

Access and documentation

Primary accessDocumentation

Repository supplies documentation and links to a multi-part SourceForge executable distribution. A repository-wide reuse license was not established; inspect distribution terms before reuse.

Evidence and review

Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.

Core publications

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

  1. A Structure-Guided Molecular Network Strategy for Global Untargeted Metabolomics Data Annotation. Analytical Chemistry (2023). doi:10.1021/acs.analchem.3c00849

Related tools

ConCISESimilar function · ConCISE propagates consensus chemical-class annotations by combining molecular-network relationships, library matches and in-silico class predictions.GNPSSimilar function · A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.GNPS2 Classical Molecular NetworkingSimilar function · GNPS2 workflow for organizing MS/MS spectra into molecular families using pairwise spectral similarity and spectral-library searching.GNPS2 Feature-Based Molecular Networking workflowSimilar function · Dedicated GNPS2 workflow that combines an aligned LC-MS feature table with MS/MS spectra to build quantitative molecular networks.

Entry history

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

  1. 2026-10-27 · First committed entry

    Add 45 source-reviewed Enveda tool entries in third expansion batch

    View change · Entry at this revision

Full GitHub history