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Preprocessing and feature extraction

Met4DX

Process LC-ion-mobility-MS data across supported four-dimensional acquisition modes.

LC-MSR packageSource available with restrictions
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Overview

Met4DX provides R workflows for feature detection, MS/MS generation and annotation in supported PASEF-DDA, PASEF-DIA and IM-AIF datasets.

What can this tool do?

Peak or feature detectionMS/MS processing

Common uses

  • Process LC-ion-mobility-MS data across supported four-dimensional acquisition modes.

Scientific fit

Primary function

Preprocessing and feature extraction

Data compatibility

Inputs

Raw instrument data, Compound list or annotations

Outputs

Feature or peak table, Mass spectra

Input formats

Instrument-specific .d data or converted IM-AIF mzML, with mode-specific tables

Output formats

Processed feature tables and generated MS/MS spectra

Scope and considerations

Designed for

  • Met4DX provides R workflows for feature detection, MS/MS generation and annotation in supported PASEF-DDA, PASEF-DIA and IM-AIF datasets.

Not designed for

  • Universal processing of arbitrary ion-mobility instruments or unverified metabolite identification.

Important requirements

  • Supported timsTOF or Agilent DTIM-MS acquisition and the documented R/Docker environment.
  • Precursor lists for list-driven modes; CCS calibration coefficients for IM-AIF.

Considerations

  • Annotation-library and retention-time calibration requirements depend on the workflow selected.

Access and documentation

Primary accessDocumentation

Repository LICENCE specifies CC BY-NC-ND 4.0, including noncommercial and no-derivatives restrictions. Public availability is not an unrestricted open-source license.

License: CC-BY-NC-ND-4.0

Evidence and review

Enveda intake checked against official documentation, license information and primary DOI/title/year on 2026-10-22. Editorial review only; no execution or independent benchmark.

Core publications

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

  1. Met4DX: A Unified and Versatile Data Processing Tool for Multidimensional Untargeted Metabolomics Data. Journal of the American Society for Mass Spectrometry (2024). doi:10.1021/jasms.4c00290

Related tools

asariSimilar function · Process high-resolution mass-spectrometry data into aligned feature tables.AutoCCSSimilar function · An open-source Python tool for calculating and calibrating experimental collision cross sections from ion-mobility mass-spectrometry data across drift-tube and traveling-wave workflows.BreathXplorerSimilar function · breathXplorer processes high-resolution breath mass-spectrometry data with feature extraction, alignment and breath-recognition functions.CAMERASimilar function · Group and annotate related LC-MS signals after XCMS peak detection.

Entry history

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

  1. 2026-10-22 · First committed entry

    Add Met4DX GNN-RT FastEI and SMQVP with verified scope

    View change · Entry at this revision

Full GitHub history