Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Quality control and filtering

RawHummus

Inspect LC-MS instrument logs and raw QC measurements through an R Shiny interface.

LC-MSR packageWeb applicationOpen source
Access toolSuggest an update

Overview

RawHummus summarizes chromatographic and MS-level quality measurements to help inspect system performance. It produces interactive QC reports and supports local execution; detecting a problem does not automatically correct the underlying data.

What can this tool do?

Interactive dashboard

Common uses

  • Inspect run-to-run variation before downstream interpretation.

Scientific fit

Primary function

Quality control and filtering

Data compatibility

Inputs

Mass spectra

Outputs

Human-readable report

Input formats

Supported raw QC measurements and instrument log files

Output formats

Interactive HTML quality reports

Scope and considerations

Designed for

  • Inspect LC-MS instrument logs and raw QC measurements through an R Shiny interface.

Not designed for

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

Important requirements

  • Representative QC measurements and an R/Shiny environment for local use.
  • Supported raw QC measurements and instrument log files; consult the app instructions for instrument-specific import

Considerations

  • The documented free hosted deployment has memory limits; local execution is recommended for larger sets.
  • Thresholds are diagnostic aids, not universal acceptance criteria.

Access and documentation

Primary access

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.

  1. RawHummus: an R Shiny app for automated raw data quality control in metabolomics. Bioinformatics (2022). doi:10.1093/bioinformatics/btac040

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