Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Quality control and filtering

mzQuality

An R package for metabolomics study quality control, including outlier detection, pooled-QC batch correction, reliability filtering, diagnostic visualization, and reporting.

Platform-independentTargeted metabolomicsUntargeted metabolomicsR packageOpen source
Access toolSuggest an update

Overview

mzQuality evaluates processed quantitative MS studies using compound abundances, sample annotations and QC information. It computes QC metrics, supports pooled-QC batch correction and calibration-based quantification, and flags compounds or samples for inspection.

What can this tool do?

Batch-effect correctionQC-based drift correctionCalibration-curve quantification

Common uses

  • Flag unreliable compounds and samples before downstream analysis.
  • Apply pooled-study-QC-based batch correction and inspect batch behavior.
  • Generate QC plots and reporting outputs for processed metabolomics tables.

Scientific fit

Primary function

Quality control and filtering

Other functions

Normalization and batch correction, Visualization and reporting, Quantification and targeted analysis

Analysis types

Targeted metabolomics, Untargeted metabolomics

Data compatibility

Inputs

Feature or peak table, Sample metadata

Outputs

Feature or peak table, Human-readable report, Statistical results

Input formats

CSV or TSV

Output formats

SummarizedExperiment with metrics, selection flags and plot objects

Scope and considerations

Designed for

  • Quality assessment and filtering of processed metabolomics studies represented as tabular abundance data.

Not designed for

  • Raw spectral feature extraction or correction of study designs lacking the reference samples required by a selected metric.

Important requirements

  • R/Bioconductor dependencies and correctly structured tabular data or a SummarizedExperiment; pooled study-QC samples are needed for QC-based correction and calibrants for concentration calculations.

Considerations

  • Thresholds and reference-sample design determine which metrics are meaningful; flagged observations need experimental context before exclusion.

Access and documentation

Primary accessDocumentation

GPL-3.0 R package. The companion mzQualityDashboard is a separately installed interactive front end; it is not part of every package-only analysis.

License: GPL-3.0

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

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

  1. mzQuality: An Open-Source Software Tool for Quality Monitoring and Reporting of Targeted Mass Spectrometry Measurements. Journal of the American Society for Mass Spectrometry (2025). doi:10.1021/jasms.5c00073

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. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history