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MSProfile.bin

Binary payload file containing profile-mode (full-scan) mass spectra. Only present when the instrument was configured to record profile data. In all corpus files tested, if MSProfile.bin exists with non-zero size, the corresponding MSScan.bin scan records have a SpectrumFormatID=1 block pointing into it.

Status: Confirmed​

File Layout​

  • Global header: 68 bytes. The first 4 bytes are an int32 magic number/version flag: 258 (0x02 0x01 0x00 0x00). The remaining 64 bytes are all zeros padding.
  • Data payload: Contiguous compressed scan blocks.

Profile Block Encoding​

  • PointCount: number of intensity values in the uncompressed block. Read from MSScan.bin scan record.
  • Compression: Profile blocks are compressed using the standard LZF algorithm.
  • The uncompressed data is an array of 32-bit integers (int32) representing raw intensity counts (e.g., ADC hits: 0, 1, 2, 3...). It is NOT an array of floats.
  • UncompressedByteCount: The exact size of the uncompressed data in bytes. This will typically be PointCount * 4 + 16 (to account for the preamble and padding).

Block Byte Structure​

  1. Preamble (16 bytes):
    • The block starts with a 16-byte fixed preamble.
    • Example (PXD001310): 07 00 00 00 00 80 d6 d4 40 20 06 20 00 01 e0 3f
    • These 16 bytes are NOT part of the LZF compressed stream.
  2. LZF Compressed Payload:
    • Starts exactly at byte offset 16 within the block.
    • It is a raw LZF stream (no frame headers like ZV, which is why standard command-line tools fail to decompress it out-of-the-box).
    • Decompressing this raw stream using the standard LZF algorithm yields exactly UncompressedByteCount bytes.
  3. Uncompressed Structure:
    • The uncompressed stream is simply an array of 32-bit integers.
    • The first 16 bytes (4 integers) of the decompressed data are typically all zeros padding.
    • The remaining integers correspond sequentially to the intensities of the profile points.
    • The m/z axis is not stored; it is a regular grid inferred from the scan's MinX and MaxX parameters divided by PointCount.