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MSMassCal.bin

Binary mass calibration file. Present only in Q-TOF acquisitions in the corpus. Stores per-scan dynamic recalibration coefficients that refine the default calibration stored in DefaultMassCal.xml.

Status: Confirmed​

File Layout​

  • Global header: 72 bytes (derived from (FileSize - 72) / NumOfScans = 84 with zero remainder for PXD001310, n=13301 scans).
  • Record stride: 84 bytes.
  • Record count: Exactly equals the number of scans in MSScan.bin (one calibration record per scan).

Record Layout (84 bytes, little-endian)​

BytesFieldType
0-3NumCoefficientsint32 (always 10 in PXD001310)
4-83Coefficients[0..9]double[10] (8 bytes each = 80 bytes)

The 10 coefficients encode two calibration steps, matching the structure in DefaultMassCal.xml:

  • Coefficients[0..1]: CalibrationFormula=Traditional (2 coefficients). For the Traditional formula, coeff[0] = A and coeff[1] = B in the Agilent Q-TOF calibration relation. Coeff[0] (A) varies slightly per scan as the dynamic recalibration corrects for instrumental drift.
  • Coefficients[2..9]: CalibrationFormula=Polynomial (8 coefficients, last 2 are always 0.0).

Calibration Coefficient Drift (PXD001310)​

Across 13301 scans, coeff[0] (the Traditional A parameter) varies from 0.0003479961 to 0.0003479973. The default XML value is 0.000347994641. The per-scan variation is ~3.48 ppm of the coefficient magnitude - this is the dynamic mass recalibration adjustment applied during acquisition (e.g., via a co-eluting reference mass lock compound).

All other 9 coefficients remain identical to the DefaultMassCal.xml values across all scans in PXD001310.

Calibration Application Note​

The calibration coefficients stored in this file are already applied to the centroid data stored in MSPeak.bin by the Agilent acquisition firmware/software prior to disk write. The mz_raw values in MSPeak.bin are fully calibrated (stored as mz * 100 retaining full double precision). Therefore, these coefficients are recorded for traceability and metadata purposes, but are not required to be manually applied to the raw flight times or raw m/z values to read the final centroid spectra.

Corpus Evidence​

  • PXD001310 (G6550A Q-TOF): header=72, stride=84, records=13301. Record 1 coefficients match DefaultCalibration DefaultCalibrationID="1" in DefaultMassCal.xml to full double precision. Record 2 matches DefaultCalibrationID="1" for coeff[1..9] and differs only in coeff[0] by the drift value documented above.
  • PXD004747 (QQQ): No MSMassCal.bin present - consistent with QQQ not using TOF-specific mass calibration.

Unresolved​

  • The exact meaning of the 72-byte header is not yet mapped.