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Legacy .wiff CFBF container

Status: Confirmed​

.wiff files use the Microsoft Compound File Binary Format (CFBF/OLE2) to store hierarchical metadata, method configuration, sample details, and the scan index for the paired .wiff.scan file. The container is structured into two main subtrees.

Method subtree (MethodSubtree/)​

Structured directory of instrument methods:

  • Method1/MethodHeader - general acquisition method metadata.
  • Method1/GLPTables - Good Laboratory Practice audit records.
  • Method1/DeviceMethodX/ - per-hardware-component configuration (LC pumps, autosamplers, MS), including PeriodX/ExperimentY/ blocks with the core MS method details (MRM transition lists, SWATH windows, source voltage/gas settings). ExperimentTOF blocks are TripleTOF- specific; sMRM/sMRMEX blocks are QTRAP-specific.

Sample subtree (SampleSubtree/)​

Tracks the execution of a specific sample acquisition:

  • SampleTable, SampleIdxTable, DabsInfo - high-level sample list and indexing.
  • Sample1/Idx - the scan index. Maps scan indices to byte ranges in the paired .wiff.scan file. See Legacy .wiff.scan blocks for its record layout.
  • Sample1/DDERealTimeData, DDERealTimeDataEx - real-time MS metadata, including precursor m/z for data-dependent MS2 scans. Not yet decoded by this reader - see Reader.
  • Sample1/SampleDABE/CFR_INFO - 21 CFR Part 11 compliance data (electronic signatures, record protection).
  • Sample1/TDCStatistics, TOFCalibrationData - TOF calibration telemetry, prominent in TripleTOF files.

Instrument variations​

TripleTOF: heavy use of TOF-specific calibration telemetry (TOFCalibrationData, TDCStatistics) and ExperimentTOF method blocks; often includes Information Dependent Acquisition (IDA) configuration.

QTRAP: heavy use of scheduled MRM configuration (sMRM, sMRMEX) and QTRAP-specific experiment headers.

Relationship to .wiff2​

The compliance-auditing streams here (CFR_INFO for 21 CFR Part 11, GLPTables for GLP) are the direct historical precedent for .wiff2: SCIEX later consolidated this entire structure into a single SQLCipher-encrypted database, natively satisfying the same compliance requirements by denying external read/write access to the metadata without the vendor SDK. See .wiff2 container.