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Scan data

Reader decodes each spectrum differently depending on which of the three on-disk variants the file is. This page is the reader-facing summary; see Format specification for the byte-level layout each summary below refers to.

.qgd GC-MS​

Every scan in GCMS Raw Data/MS Raw Data starts with a 32-byte header, located via the Spectrum Index stream. Two acquisition modes exist:

  • Full-scan profile mode: the payload is N_Peaks interleaved (m/z, intensity) u16 pairs (m/z scaled by 10). The reader yields one MS1 SpectrumRecord per scan.
  • MRM/targeted mode: the payload is a sequence of monitored transitions, each (precursor m/z, product m/z, intensity) with a variable intensity byte width read directly from the scan header. The reader yields one MS2 SpectrumRecord per transition (a single (product_mz, intensity) point, with the precursor's m/z carried in PrecursorInfo) rather than trying to force multiple simultaneously monitored transitions into a single spectrum.

See GC-MS (.qgd) for the full byte layout.

.lcd IT-TOF​

Every scan in TTFL Raw Data/MS Raw Data is a variable-length metadata prefix followed by a run-length-encoded sparse array of 16-bit intensity samples over an implicit index axis. The reader reconstructs (position, intensity) pairs from the RLE stream and exposes position directly as mz - it is not calibrated m/z, just a raw digitizer time-bin index (see Known limitations). Four interleaved acquisition channels (sub_i 0-3) are tracked per retention-time point via the Data Index stream, but the reader does not currently map any channel to a specific polarity or MS level.

See LC-MS IT-TOF (.lcd) for the full byte layout.

.lcd QTOF​

Every scan in QTFL RawData/Centroid Data is a 64-byte header followed by an N-element u64 m/z array (scaled by 10^12) and an N-element intensity array whose byte width (1, 2, or 4 bytes) is read from the scan header - it is not always 16-bit. Centroid Index's per-scan event_id field distinguishes MS1 (event_id == 1) from MS2 (event_id > 1) scans within each acquisition cycle; MS2 records carry a reference to their parent MS1 scan but not a decoded precursor m/z.

See LC-MS QTOF (.lcd) for the full byte layout.

Retention time​

retention_time_sec is derived from each format's own Retention Time stream (milliseconds for .lcd, matched against the scan header's own copy of the value for IT-TOF).

Fields not yet populated​

Polarity is None for every spectrum in every variant - see Known limitations for the full list of what each format still leaves open.