Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Quantification and targeted analysis

Skyline

Develop and review targeted mass-spectrometry assays, including small-molecule quantification.

LC-MSDesktop graphical interfaceSource available with restrictions
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Overview

Skyline supports chromatogram inspection, transition-based methods, calibration and quantitative reporting. Dedicated tutorials cover metabolomics and lipidomics applications.

What can this tool do?

Calibration-curve quantificationChromatogram building

Common uses

  • Review targeted small-molecule peak integration.
  • Quantify analytes using external calibration and internal standards.

Scientific fit

Primary function

Quantification and targeted analysis

Data compatibility

Inputs

Raw instrument data, Compound list or annotations

Outputs

Feature or peak table, Human-readable report

Input formats

Vendor raw format

Output formats

CSV or TSV

Scope and considerations

Designed for

  • Review targeted small-molecule peak integration.

Not designed for

  • Unrestricted discovery of all unknown compounds in a raw file.

Important requirements

  • A compatible installation, assay targets and supported measurement files.

Considerations

  • Confirm transition specificity, calibration range and internal-standard behavior before reporting concentrations.

Access and documentation

Primary access

Software source is distributed through ProteoWizard; consult component and vendor-reader terms.

From tool to strategy

Strategies using Skyline

Reference-pool discovery with cohort-wide signal extractionPhenotype association · Analytical Chemistry

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. MacLean B, Tomazela DM, Shulman N, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968 (2010). doi:10.1093/bioinformatics/btq054

    Foundational Skyline software paper, originally scoped to targeted proteomics. Consult the linked small-molecule documentation for metabolomics workflows.

Software and documentation citations

  • Skyline team. Small Molecule Quantification and Small Molecules tutorials. Official Skyline documentation. Documentation

Related tools

lipidrComplementary to · Analyze lipid abundance tables and test patterns across lipid classes and structural properties.SmartPeakComplementary to · Automate targeted and semi-targeted chromatographic data processing and quantification.LipidCreatorIntegrates with · Design targeted lipidomics assays and predicted fragment libraries for PRM and MRM experiments.

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