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GC-MS (.qgd)

Status: Partial​

The GCMS Raw Data storage in .qgd files holds all mass-spectrometry data. Two distinct data encodings exist, corresponding to different acquisition modes.

Spectrum Index​

GCMS Raw Data/Spectrum Index maps sequential scan numbers to byte offsets in MS Raw Data. Two on-disk variants have been observed:

  • No header: an array of u32 (LE) absolute byte offsets. Scan count is stream_size / 4.
  • 2-byte header (u16 LE, typically 1): an array of u64 (LE) absolute byte offsets. Scan count is (stream_size - 2) / 8.

MS Raw Data scan header​

Every scan begins with a 32-byte header of mostly u32/u16 fields: scan index/flags, retention time (matching the Retention Time stream), a scan number, and a pair of format/event-ID/peak-count fields whose exact byte placement depends on which acquisition mode the scan is (see below).

Full-scan profile mode​

The payload following the header is N_Peaks interleaved (m/z, intensity) u16 pairs. m/z is scaled by 10 (raw 1000 = 100.0 Da). Scan size validates exactly as 32 + N_Peaks * 4 bytes.

MRM / targeted mode​

Represents scheduled Multiple Reaction Monitoring on a triple-quad GC-MS/MS instrument. The scan header's Event ID field distinguishes acquisition "events" (segments), which can interleave within a run. The payload is a sequence of transitions, each encoded as [precursor m/z (u16, x10)] [product m/z (u16, x10)] [intensity (variable-width LE int)].

The intensity byte width is not guessed by dividing the payload size against candidate widths - it's read directly from the scan header's N_Peaks/Event-ID slot, which for this mode holds the literal transition count, letting the reader compute intensity_width = data_bytes / n_transitions - 4 exactly. Within one nominal Event ID, the actual monitored (precursor, product) pairs can differ scan-to-scan (real MRM time-multiplexing across a segment with more logical transitions than fit in a single scan's dwell cycle, not a decode error).

Not yet resolved​

  • Polarity: no polarity bit has been found in either the 32-byte scan header or the Spectrum Index stream. GC-EI-MS is conventionally positive-ion, but that's a domain convention, not a decoded field, so it's left unpopulated - see Known limitations.
  • Instrument model: no per-file instrument-model string has been found decoded anywhere in the corpus.

See docs/format/02-gcms-qgd-scans.md in the repository for the full byte-level record, including the per-event intensity-width table derived from the reference corpus file.