Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Spectral processing and comparison

MSnbase

Manipulate, process and visualize mass-spectrometry data within R.

Multiple analytical platformsR packageOpen source
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Overview

MSnbase supplies data classes and functions spanning spectra and quantitative measurements. It is infrastructure used in analytical workflows, including metabolomics.

What can this tool do?

MS/MS processing

Common uses

  • Inspect and manipulate spectra programmatically.
  • Maintain compatibility with R workflows built around MSnbase objects.

Scientific fit

Primary function

Spectral processing and comparison

Data compatibility

Inputs

Mass spectra, Feature or peak table

Outputs

Mass spectra, Feature or peak table

Input formats

Other, Spectra and MSnbase quantitative objects

Output formats

Other, MSnbase spectral and quantitative objects

Scope and considerations

Designed for

  • Inspect and manipulate spectra programmatically.

Not designed for

  • A ready-made end-to-end metabolomics pipeline without additional methods.

Important requirements

  • R/Bioconductor and data compatible with the package import functions.

Considerations

  • Check object compatibility when combining older MSnbase workflows with newer Spectra-based packages.

Access and documentation

Primary access

Open-source software; use the official installation, license and citation guidance for the selected release.

Evidence and review

Documentation-based editorial review on 7 September 2026. Scope and limitations summarize the linked official sources; software execution and developer verification were not assessed.

Core publications

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

  1. Gatto L, Lilley KS. MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics 28, 288-289 (2012). doi:10.1093/bioinformatics/btr645

    Foundational MSnbase software paper; the original publication focuses on isobaric tagged mass spectrometry.

Software and documentation citations

  • MSnbase developers. MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics. Bioconductor package record. doi:10.18129/B9.bioc.MSnbase

Related tools

SpectraComplementary to · Store, filter, process and compare mass spectra through a common R interface.ParamounterIntegrates with · Estimate LC-MS processing parameters from measured data for downstream feature extraction.peakPantheRIntegrates with · R package for targeted extraction and integration of predefined metabolic features across LC-MS profiling files.

Entry history

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

  1. 2026-09-08 · Entry update

    Audit core publications across existing tools

    View change · Entry at this revision
  2. 2026-09-07 · First committed entry

    Add 50 documented metabolomics resources

    View change · Entry at this revision

Full GitHub history