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Isotope tracing and flux analysis

isoSCAN

Integrate stable-isotope-labeling peaks from GC chemical-ionization mass spectrometry data.

GC-MSR packageOpen source
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Overview

isoSCAN is an R package for automatic peak integration in low- and high-resolution GC-CI-MS labeling experiments. Its catalogue scope follows the official package description; LC-MS support is not inferred from the discovery list.

What can this tool do?

Peak or feature detection

Common uses

  • Process GC-CI-MS measurements from stable-isotope experiments.

Scientific fit

Primary function

Isotope tracing and flux analysis

Data compatibility

Inputs

Mass spectra, Isotope-tracing data

Outputs

Isotope-tracing data

Input formats

GC-CI-MS labeling data supplied through the documented R workflow

Output formats

Integrated isotope-labeling peak measurements returned by the R workflow

Scope and considerations

Designed for

  • Peak integration for GC chemical-ionization labeling data.

Not designed for

  • A general LC-MS workflow or independent confirmation of metabolic flux.

Important requirements

  • GC-CI-MS measurements and the repository R dependencies; consult the package vignette for import preparation.

Considerations

  • Match ionization mode and isotope experiment to the documented workflow.

Access and documentation

Primary access

R package depending on mzR and other packages declared in DESCRIPTION.

License: GPL-3.0

Evidence and review

Discovered through the Enveda review intake; official repository and primary publication metadata checked on 2026-10-02. Editorial review only; software and performance not execution-tested.

Core publications

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

  1. Exploring the Use of Gas Chromatography Coupled to Chemical Ionization Mass Spectrometry (GC-CI-MS) for Stable Isotope Labeling in Metabolomics. Analytical Chemistry (2020). doi:10.1021/acs.analchem.0c02998

    Published online December 2020; journal issue 2021. Both dates can appear in citations.

Related tools

13C-SpaceM analysis codeSimilar function · Analyze spatial carbon-13 labeling of fatty acids in single cells and tissue imaging experiments.AerithSimilar function · An R package for reading, annotating, scoring, and visualizing isotopic mass spectra in stable-isotope-probing workflows for metabolites and peptides.FAMetASimilar function · Estimate fatty-acid synthesis, import, elongation and desaturation from carbon-13 isotopologue profiles.IsoPairFinderSimilar function · An R package for identifying biologically relevant 12C/13C feature pairs in stable-isotope-tracing metabolomics, including differential analysis and redundant-feature merging.

Entry history

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

  1. 2026-10-02 · First committed entry

    Add five source-verified isotope and spatial tools from Enveda intake

    View change · Entry at this revision

Full GitHub history