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Shimadzu LabSolutions

Shimadzu LabSolutions .qgd (GC-MS) and .lcd (LC-MS) files are read by openszraw, a pure-Rust reader for the CFBF-container LabSolutions formats, clean-room reverse-engineered with no Shimadzu SDK or software dependency. It covers GC-MS (full-scan profile and MRM/targeted acquisition) and LC-MS across both the IT-TOF and QTOF (LCMS-9030) instrument families.

Detection​

A path is treated as Shimadzu when:

  • the filename has a .qgd or .lcd extension (case-insensitive), and
  • its first 8 bytes are the CFBF/OLE2 container signature.

Unlike SCIEX's .wiff/.wiff.scan pair, Shimadzu raw files are self-contained - there is no sibling file to corroborate against, so the magic-byte check is the only content-level signal used. openszraw::reader::Reader further distinguishes .qgd GC-MS from .lcd IT-TOF from .lcd QTOF internally, from the file's own CFBF stream layout, never from the filename alone - so a single shimadzu feature and VendorFormat variant covers all three.

Covered features​

  • .qgd GC-MS: full-scan profile and MRM/targeted acquisition.
  • .lcd IT-TOF: run-length-encoded profile spectra, calibrated to physical m/z from the file's own embedded TOF tuning data.
  • .lcd QTOF (LCMS-9030): centroid spectra.
  • Indexed mzML with native-id format Shimadzu Biotech nativeID format (MS:1000929) or Shimadzu Biotech QTOF nativeID format (MS:1002898), depending on variant.

Known gaps​

  • QQQ (triple-quadrupole) .lcd files use a distinct TLM Raw Data storage that is not yet decoded - see OpenSZRaw issue #5.
  • PDA/UV chromatogram streams (PDA 3D Raw Data, LSS Raw Data) are not decoded or exposed - see OpenSZRaw issue #2.
  • IT-TOF per-channel polarity/MS-level and QTOF MS2 precursor m/z are not yet resolved. See OpenSZRaw's known-limitations doc for the full, evidence-backed list.

Tested instruments​

The conformance suite is tested against a real corpus spanning IT-TOF, QTOF (LCMS-9030), and GC-MS/GC-MS-MS instrument families across PRIDE, MassIVE, and MetaboLights accessions - see OpenSZRaw's CORPUS.md.

See also​