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Agilent MassHunter

Agilent .d/ directories are read by openaraw, a pure-Rust reader for the MassHunter AcqData on-disk layout, clean- room reverse-engineered with no Agilent SDK or MassHunter runtime.

Detection​

A path is treated as Agilent when:

  • it is a directory, and
  • it contains AcqData/MSScan.bin.

Bruker TDF bundles are also commonly named <run>.d/, so detect_format checks for the Bruker signature (analysis.tdf + analysis.tdf_bin) first; a bundle only falls through to the Agilent check once that fails. See Format detection for the full ordering.

Covered features​

  • Q-TOF acquisitions: profile and centroid MS1/MS2.
  • QQQ (MRM) acquisitions, including per-transition precursor and product native IDs.
  • Indexed mzML with native-id format Agilent MassHunter nativeID format (MS:1002848).

Known gaps​

  • polarity and the MS2 selected_mz (distinct from the isolation- window target_mz) are always None. Both were checked directly against the corpus - including a confirmed mixed-polarity run in PXD031771 - and no recoverable field was found in MSScan.bin or MSPeriodicActuals.bin. See OpenARaw's known-limitations notes for the byte-level investigation.
  • A handful of PRIDE-hosted .d uploads are structurally malformed (missing AcqData entirely, or are macOS __MACOSX artifacts) and are excluded from the conformance corpus rather than misreported.

Tested instruments​

The conformance suite is validated against 332 of 338 real-world PRIDE .d datasets, covering Q-TOF (profile and centroid) and QQQ (MRM) acquisitions; the remaining 6 are the malformed uploads above, not reader gaps.

See also​