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Bruker timsTOF TDF

Bruker .d/ bundles are read by opentimstdf, which parses the SQLite metadata in analysis.tdf and the binary frame data in analysis.tdf_bin without calling Bruker's libtimsdata.

Detection​

A path is treated as Bruker when:

  • the directory name ends in .d (case-insensitive), and
  • the directory contains both analysis.tdf and analysis.tdf_bin.

Covered features​

  • TIMS-on and TIMS-off acquisitions (timsTOF Pro, fleX, Pro 2, HT).
  • MS1, PASEF MS/MS, dia-PASEF.
  • Per-peak inverse ion mobility array (Arrow inv_mobility_per_peak).
  • Frame-merged MS1 spectra (one row per frame) plus per-precursor PASEF MS2 spectra.
  • Indexed mzML with native-id format Bruker TDF nativeID format.

Known gaps​

  • MALDI / imaging acquisitions (MaldiFrameInfo-based) are out of scope for the mzML writer in 0.x; the data is reachable via the lower-level opentimstdf API.
  • IMS-MS quadrupole-window calibration is reported but not validated against vendor-side calibration curves.

Tested instruments​

The conformance suite exercises timsTOF Pro, fleX, Pro 2, and HT acquisitions from public PRIDE datasets.

See also​