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Data conversion and import

OpenTIMS

Read Bruker timsTOF TDF data through C++, Python or R interfaces.

LC-MSPython packageR packageOpen source
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Overview

OpenTIMS is a data-access library for Bruker timsTOF TDF files with Python and R bindings. It exposes frame, scan, time-of-flight and intensity data, plus calibrated m/z and inverse-mobility coordinates through the documented conversion routes.

What can this tool do?

Spectral data reading and writing

Common uses

  • Read timsTOF TDF data into Python or R for downstream analysis.

Scientific fit

Primary function

Data conversion and import

MS level

MS1, MS/MS

Acquisition

General or unspecified acquisition

Ion mobility

Ion mobility supported

Data compatibility

Inputs

Raw instrument data

Outputs

Mass spectra

Input formats

Vendor raw format

Output formats

NumPy arrays, R data frames or C++ data structures with spectral coordinates

Scope and considerations

Designed for

  • Programmatic access to Bruker timsTOF TDF data.

Not designed for

  • Complete metabolomics preprocessing, molecular annotation or universal support for all Bruker data formats.

Important requirements

  • A TDF directory containing both analysis.tdf and analysis.tdf_bin, and an appropriate Python/R installation or C++ build environment. Source builds need the documented compiler and library dependencies.

Considerations

  • Choose conversion/calibration behavior explicitly and record it. Large all-frame queries may exceed memory; selected columns or frame iteration can reduce resource use.

Access and documentation

Primary accessDocumentation

MIT core with third-party notices. The optional Bruker bridge distributes proprietary conversion binaries under separate terms; current open-source conversion can also be selected.

License: MIT

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. OpenTIMS, TimsPy, and TimsR: Open and Easy Access to timsTOF Raw Data. Journal of Proteome Research (2021). doi:10.1021/acs.jproteome.0c00962

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