Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Preprocessing and feature extraction

MS-DIAL

A graphical and command-line workbench for untargeted metabolomics and lipidomics data processing across multiple chromatography and mass spectrometry platforms.

LC-MSGC-MSCE-MSDirect-infusion MSMALDI-MS
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Overview

MS-DIAL is a metabolomics and lipidomics workbench designed for broad-spectrum processing of chromatography–mass-spectrometry datasets. It combines peak detection, deconvolution, alignment, spectral annotation, normalization, statistics, and visualization, with particular support for data-independent MS/MS processing and lipid annotation.

Also known as: MSDIAL, MS Dial

What can this tool do?

Peak or feature detectionSpectral deconvolutionRetention-time alignmentGap fillingAdduct and isotope groupingSpectral-library matchingMS/MS processingMultivariate statistics

Common uses

  • Process untargeted LC-MS, GC-MS, and lipidomics datasets through a graphical workflow.
  • Deconvolute data-independent MS/MS spectra and match features against spectral libraries.
  • Export aligned abundances and representative spectra for downstream analysis while preserving feature IDs.

Scientific fit

Primary function

Preprocessing and feature extraction

Other functions

Normalization and batch correction, Metabolite annotation and identification, Spectral processing and comparison, Statistical analysis, Visualization and reporting

Analysis types

Untargeted metabolomics, Lipidomics, Stable-isotope tracing, Metabolite profiling

MS level

MS1, MS/MS

Acquisition

Full-scan MS, Data-dependent acquisition (DDA), Data-independent acquisition (DIA), All-ion fragmentation

Ion mobility

Ion mobility supported

Data compatibility

Inputs

Raw instrument data, Mass spectra, Spectral library

Outputs

Feature or peak table, Mass spectra, Compound list or annotations, Statistical results

Input formats

Vendor raw format, mzML, netCDF or CDF, MSP

Output formats

CSV or TSV, MSP, MGF, mzTab-M

Scope and considerations

Designed for

  • Broad untargeted metabolomics and lipidomics processing through a graphical workflow across several chromatography and MS acquisition modes.
  • Datasets requiring deconvolution and interpretation of data-independent or all-ion MS/MS signals.

Not designed for

  • Treating all library annotations as equally resolved molecular structures.

Important requirements

  • Users should confirm current operating-system support and input-format compatibility for the version they install.

Considerations

  • Large libraries and highly permissive annotation settings can increase candidate identifications; confidence levels and library provenance should be reported.
  • For lipidomics, report the structural level supported by the fragmentation evidence; review deconvolution and retention information for ambiguous features.

Education

Learn this tool

External tutorials and workshops collected by Navigator. Entries marked Needs review have not been checked end to end.

MassQL in MS-DIAL 5 (no audio)MS-DIAL project · Video · Needs reviewMS-DIAL 5 LC-MS/MS DDA tutorialMS-DIAL project · Video · Needs reviewMS-DIAL 5 official tutorialMS-DIAL project · Training hubMS-DIAL 5 raw data viewer tutorialMS-DIAL project · Video · Needs reviewMS-DIAL 5 to MS-FINDER for unknown annotationMS-DIAL project · Video · Needs reviewMS-DIAL and GNPS in PortugueseData Deconvolution Lab (GNPS community listing) · Video · Needs reviewMultivariate analysis in MS-DIAL 5MS-DIAL project · Video · Needs review

Browse all education resources →

Access and documentation

Primary accessSource repositoryDocumentation

The software, source, and associated libraries are publicly accessible; users should confirm the license and terms that apply to the specific component and version they use.

From tool to strategy

Strategies using MS-DIAL

Feature-Based Molecular Networking (FBMN)Molecular-family discovery · Nature Methods

Evidence and review

Documentation-based editorial pass on 6 September 2026: scope, interpretation limits and practical use reviewed against the linked official documentation and cited literature. Software execution, service availability and developer verification were not assessed.

Core publications

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

  1. Tsugawa H, Ikeda K, Takahashi M, et al. A lipidome atlas in MS-DIAL 4. Nat Biotechnol 38, 1159-1163 (2020). doi:10.1038/s41587-020-0531-2

    Introduces MS-DIAL 4 alongside the lipidome atlas; retained as a direct software update.

  2. Tsugawa H, Cajka T, Kind T, et al. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat Methods 12, 523-526 (2015). doi:10.1038/nmeth.3393

Related tools

MZmineAlternative to · A modular mass-spectrometry environment for raw-data import, feature detection/alignment, multimodal LC/IMS/GC/MSI processing, molecular networking, annotation, lipid analysis, visualization, normalization, statistics, and downstream exports.GNPSIntegrates with · A web-based mass-spectrometry ecosystem for molecular networking, spectral-library search, repository-scale search, interactive visualization, knowledgebase curation, and public-data integration.LipidBlastComplementary to · Use an in-silico tandem mass-spectral library to support lipid annotation.MS-FINDERComplementary to · Explore formula and structure candidates using fragmentation rules and EI-MS or MS/MS library searches.OpenChromComplementary to · Inspect and process chromatographic and mass-spectrometric data in a desktop workbench.GNPS2 Feature-Based Molecular Networking workflowIntegrates with · Dedicated GNPS2 workflow that combines an aligned LC-MS feature table with MS/MS spectra to build quantitative molecular networks.

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 · Entry update

    Expand and document 31 metabolomics tools and resources

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  3. 2026-08-24 · Entry update

    Apply v5.2 pre-population hardening

    View change · Entry at this revision
  4. 2026-08-21 · Entry update

    Add files via upload

    View change · Entry at this revision
  5. 2026-08-20 · First committed entry

    Add files via upload

    View change · Entry at this revision

Full GitHub history