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Data conversion and import

TIMSCONVERT

An open-source workflow for converting Bruker timsTOF raw data, including trapped-ion-mobility information, into open mzML and imzML formats for downstream analysis.

Multiple analytical platformsCommand lineDesktop graphical interfaceOpen source
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Overview

TIMSCONVERT converts supported Bruker timsTOF raw acquisitions to open mzML or imzML while retaining ion-mobility information where supported. It provides graphical and command-line routes to data conversion for downstream analysis.

What can this tool do?

Spectral data reading and writing

Common uses

  • Convert timsTOF data to open formats while preserving ion-mobility information.

Scientific fit

Primary function

Data conversion and import

MS level

MS1, MS/MS

Acquisition

General or unspecified acquisition

Ion mobility

Ion mobility required

Data compatibility

Inputs

Raw instrument data

Outputs

Mass spectra, Imaging data

Input formats

Vendor raw format

Output formats

mzML, imzML

Scope and considerations

Designed for

  • An open-source workflow for converting Bruker timsTOF raw data, including trapped-ion-mobility information, into open mzML and imzML formats for downstream analysis.

Not designed for

  • Feature extraction, metabolite identification or conversion of arbitrary proprietary vendor formats.

Important requirements

  • Supported timsTOF acquisition directories and the documented Windows/Linux environment with the required Bruker TDF-SDK components; output mode must match LC-MS or imaging acquisition.

Considerations

  • Conversion options and mobility handling must suit the acquisition and downstream reader. Preserve original raw data and record conversion parameters.

Access and documentation

Primary accessDocumentation

Apache-2.0 workflow code includes components covered by separate Bruker proprietary terms. The required TDF-SDK route is not compatible with macOS according to the project documentation.

License: Apache-2.0

Evidence and review

Enveda intake rechecked against official README/documentation, repository access terms and primary publication metadata on 2026-10-27. Editorial source review only; no software execution or independent benchmarking. See docs/enveda-expansion-review-2026-10-27.md.

Core publications

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

  1. TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats. Bioinformatics (2022). doi:10.1093/bioinformatics/btac419

Related tools

AirdProSimilar function · AirdPro converts mass-spectrometry vendor data into the Aird storage format through a graphical batch-conversion workflow.arcMSSimilar function · arcMS converts Waters UNIFI MS-E and HDMS-E data into tabular Parquet or HDF5 storage for analysis in R or Python.MobilityTransformRSimilar function · MobilityTransformR converts CE-MS migration times to an effective-mobility scale using added mobility markers.msconvertSimilar function · Convert mass-spectrometry files into open formats for downstream analysis.

Entry history

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

  1. 2026-10-27 · First committed entry

    Add 27 source-reviewed tools from Enveda intake

    View change · Entry at this revision

Full GitHub history