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LC-MS QTOF (.lcd)

Status: Confirmed for the payload shape, with corrections​

The QTFL RawData storage in 9030-series QTOF .lcd files holds centroided mass-spectrometry data. Unlike IT-TOF, QTOF uses a clean, uncompressed block layout.

Centroid Index​

24 bytes per record, mapping sequential scan events to their payload in Centroid Data: an absolute byte offset, a subset/interleave index, a global event counter, a local scan index, and a segment/event ID. A scan's byte length is derived by subtracting its offset from the next chronological scan's offset.

The segment/event ID field is a real per-acquisition-cycle counter, not an opaque tag: event_id == 1 is the MS1 survey scan, and event_id > 1 are MS2 product-ion scans (1-4 observed per cycle in the corpus), consistent with DDA acquisition selecting a variable number of precursors per cycle.

Centroid Data payload​

Every scan begins with a 64-byte header, including the base-peak intensity and the data payload size in bytes. The payload itself is:

  1. An N-element array of u64 (LE) m/z values, scaled by 10^12 (mz = u64_value / 1e12).
  2. An N-element intensity array.

N is payload_size / (8 + width), where width (1, 2, or 4 bytes) is read from the scan header rather than assumed fixed. Treating intensity as always 16-bit produces a confirmed corrupt decode on higher-dynamic-range (mostly MS2) scans - verified by cross-checking max(intensity) against the header's declared base-peak intensity across every non-empty scan in the reference corpus file: zero mismatches once width is read per-scan, versus spurious values and a base-peak mismatch when assumed fixed at 2 bytes.

Not yet resolved​

  • MS2 precursor m/z: the real per-scan precursor m/z for MS2 events lives in the separate QTFL RawData/DDA stream, which has not been decoded. The reader classifies ms_level from event_id and populates MS2 PrecursorInfo with only a reference to the parent MS1 scan, not a decoded m/z - see Known limitations.

See docs/format/05-qtfl-centroid.md in the repository for the full byte-level record.