Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Quality control and filtering

QC4Metabolomics

Monitor LC-MS data quality with a configurable processing service, database and dashboard.

LC-MSWeb applicationOpen source
Access toolSuggest an update

Overview

QC4Metabolomics provides a locally deployed QC system with background processing, a MariaDB database and a Shiny interface. Its MetabolomiQCsR component supplies QC functions. Optional conversion services prepare mzML inputs.

Also known as: MetabolomiQCsR

What can this tool do?

Container supportInteractive dashboard

Common uses

  • Track quality measurements across acquisitions.

Scientific fit

Primary function

Quality control and filtering

Data compatibility

Inputs

Mass spectra, Sample metadata

Outputs

Human-readable report

Input formats

mzML files plus configured file-name metadata and QC settings

Output formats

QC database records and dashboard views

Scope and considerations

Designed for

  • Monitor LC-MS data quality with a configurable processing service, database and dashboard.

Not designed for

  • Confirming compound identity or replacing study design and scientific review.

Important requirements

  • Docker/Compose, configured data volumes, database and background workers.

Considerations

  • This is infrastructure to deploy and configure, not simply a public upload website.
  • File naming and metadata parsing must match the local acquisition setup.

Access and documentation

Primary accessSource repository

License checked against official package metadata or repository. Local setup requires the documented dependencies; no installation or hosted-service availability test was performed.

License: GPL-3.0-or-later

Evidence and review

Enveda intake candidate verified against official documentation, source/package metadata and primary-publication DOI/title/year on 2026-10-02. Editorial review only; no software execution or independent benchmark.

Core publications

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

  1. QC4Metabolomics: Real-Time and Retrospective Quality Control of Metabolomics Data. Analytical Chemistry (2025). doi:10.1021/acs.analchem.4c07078

Related tools

dbnormSimilar function · Compare statistical batch-correction models and inspect technical variation in metabolomics matrices.InjectionDesignSimilar function · A web service for designing LC-MS and GC-MS multi-omics injection sequences with QC placement, inter-batch balancing, intra-batch randomization, and downloadable worksheets.IonToolPackSimilar function · IonToolPack groups graphical mass-spectrometry utilities for raw-data visualization, PeakQC quality assessment, tandem-library matching, targeted MS1 extraction and feature-list comparison.ISFragSimilar function · ISFrag recognizes candidate in-source fragments in LC-MS data by combining feature relationships and available MS/MS evidence.

Entry history

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

  1. 2026-10-05 · First committed entry

    Add seven source-validated QC tools and Enveda intake ledger

    View change · Entry at this revision

Full GitHub history