Overview
MsQuality uses the mzQC controlled vocabulary to calculate low-level quality metrics from Spectra or MsExperiment objects. It supports tracking data quality across runs but is not itself a signal-drift correction algorithm.
What can this tool do?
Common uses
- Calculate comparable low-level QC summaries for MS-metabolomics runs.
Scientific fit
Primary function
Quality control and filtering
Data compatibility
Inputs
Mass spectra
Outputs
Human-readable report
Input formats
Spectra or MsExperiment objects
Output formats
Per-sample quality-metric results from the R interface
Scope and considerations
Designed for
- Calculate standardized per-sample quality metrics from mass spectrometry data in R.
Not designed for
- Confirming compound identity or replacing study design and scientific review.
Important requirements
- A compatible R/Bioconductor installation and populated spectral objects.
- Spectra or MsExperiment objects with retention time, m/z and intensity information
Considerations
- Available metrics depend on the information stored in each input; low-level metrics do not replace experimental QC design.
Access and documentation
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
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.
- MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. Bioinformatics (2023). doi:10.1093/bioinformatics/btad618
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-05 · First committed entry
Add seven source-validated QC tools and Enveda intake ledger
View change · Entry at this revision