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Reader

The entry point is Reader. Reader::open takes a path to a .qgd or .lcd file, opens it as an OLE2/CFBF container, and inspects which top-level storage is present (GCMS Raw Data, TTFL Raw Data, or QTFL RawData) to detect which of the three on-disk variants it is - never from the file extension or name. See Format variants for what distinguishes them.

use openszraw::reader::Reader;

let reader = Reader::open("sample.lcd")?;

Reader implements openmassspec_core::SpectrumSource, the shared trait every vendor reader in the OpenMassSpec stack implements:

use openmassspec_core::SpectrumSource;

let metadata = reader.run_metadata();
let scan_count = reader.spectrum_count_hint().unwrap_or(0);
println!("{} ({} scans)", metadata.source_file_name, scan_count);

let mut reader = reader;
for spectrum in reader.iter_spectra() {
    println!("{}\t{}\t{} peaks", spectrum.native_id, spectrum.ms_level, spectrum.mz.len());
}

Each yielded SpectrumRecord carries index, native_id, ms_level, retention_time_sec, and mz/intensity arrays. spectrum_count_hint is exact for .lcd IT-TOF and QTOF, but only approximate for .qgd MRM data: each monitored transition within a scan expands into its own SpectrumRecord, so the real record count can exceed the raw scan count for MRM/targeted acquisitions - see GC-MS (.qgd).

What the reader does not yet do​

  • IT-TOF polarity / MS level: every IT-TOF spectrum reports ms_level = 1 and polarity = None; the channel-to-polarity mapping implied by dataset naming (..._pos-neg_NN.lcd) has not been decoded.
  • QTOF MS2 precursor m/z: MS2 spectra carry a precursor_native_id reference to the most recent MS1 scan, but not a decoded target_mz/selected_mz - the real value lives in the undecoded QTFL RawData/DDA stream.
  • .qgd polarity: not populated; no polarity bit has been found in the scan header or Spectrum Index stream.
  • PDA / chromatogram streams: PDA 3D Raw Data (the UV detector) and LSS Raw Data (chromatogram) are out of scope for this crate; their segment-level delta encoding has not been decoded - see Known limitations.

Error handling​

Public functions return openszraw::Result<T>. The error type is openszraw::Error, which wraps the failure category (Io, Parse) and a message.