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MSPeak.bin

Binary payload file containing centroid (peak) mass spectra. Present in both QQQ and Q-TOF acquisitions. Each scan's data block is located via SpectrumOffset and ByteCount from the corresponding MSScan.bin scan record.

Status: Confirmed​

File Layout​

  • Global header: 68 bytes. The first 4 bytes are an int32 magic number/version flag: 259 (0x03 0x01 0x00 0x00). The remaining 64 bytes are all zeros padding.
  • Data payload: Contiguous scan blocks, each starting at the SpectrumOffset stored in MSScan.bin.

Peak Block Encoding​

The encoding inside each block differs between QQQ and Q-TOF.

QQQ MRM (FormatID=3): Array of Structures (AoS)​

  • 12 bytes per point: double mz (8 bytes) + float intensity (4 bytes).
  • In MRM mode, PointCount is always 1 (single MRM transition per scan).
  • mz is in Da (real mass units, no scaling factor). Verified against AcqMethod.xml transition list.
  • Example (PXD004747 scan 1): mz=875.4300, intensity=41.28; (scan 2) mz=673.3700, intensity=41.26.

Q-TOF Centroid (FormatID=2): Structure of Arrays (SoA)​

  • A block of N points is NOT stored as N interleaved (mz, intensity) tuples.
  • Layout: N * double mz_raw (8 bytes each), immediately followed by N * float intensity (4 bytes each).
  • Total block size: N * 8 + N * 4 = N * 12, matching ByteCount.
  • mz encoding: mz_raw values are stored as 100x the real, fully-calibrated m/z in Da (retaining full double-precision floating point accuracy). Divide by 100.0 to get the final Da value.
    • Note: The calibration parameters in MSMassCal.bin are already applied to these values upstream by the instrument's acquisition software before they are written to disk. No further calibration math is required.
    • Verified across PXD001310 and PXD004426 by confirming that mz_raw / 100.0 falls within the scan's MinX/MaxX bounds.
  • MS2 scan centroid ions may fall outside the MinX/MaxX of the precursor scan (expected; those bounds describe the Q1/profile scan range, not the fragment window).
  • Confirmed SoA on two independent Q-TOF files:
    • PXD001310 scan 1: N=1258, block=15096 bytes (10064 + 5032). mz_raw values strictly follow double-precision fractionals (e.g., 29888.4237296802 -> 298.88423730 Da).
    • PXD004426 scan 1: N=15, block=180 bytes (120 + 60). mz_raw range: 50767-101587 -> Da: 507.7-1015.9.
  • Intensities are positive and non-zero for all non-baseline peaks (verified).

Unresolved​

  • Whether Q-TOF files from instruments other than G6550A/G6540B use the same 100x mz scale.