Overview
Paramounter supplies R scripts for parameter estimation before feature extraction. The checked script reads mzXML through MSnbase and requires XCMS. Outputs guide processing settings; they are not validated metabolite identifications.
What can this tool do?
Common uses
- Estimate mass-tolerance and peak-processing settings.
Scientific fit
Primary function
Preprocessing and feature extraction
Data compatibility
Inputs
Mass spectra
Outputs
Human-readable report
Input formats
mzXML files read by the supplied R scripts
Output formats
Parameter estimates and diagnostic plots for configuring downstream processing
Scope and considerations
Designed for
- Estimate LC-MS processing parameters from measured data for downstream feature extraction.
Not designed for
- Confirming compound identity or replacing study design and scientific review.
Important requirements
- R with XCMS, MSnbase and the other script dependencies; edit example file paths and review the supplied manual.
Considerations
- The repository warns that permissive optimized peak thresholds may increase false positives or cause crashes.
- The available implementation is a script workflow, not a verified installable R package.
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: MIT
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.
- Paramounter: Direct Measurement of Universal Parameters To Process Metabolomics Data in a “White Box”. Analytical Chemistry (2022). doi:10.1021/acs.analchem.1c04758
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
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