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Reader

The entry point is Reader. Reader::open takes a path to the .wiff file, opens it as a CFBF container, reads the SampleSubtree/Sample1/Idx stream up front to build the full scan index, and expects the paired .wiff.scan file (same name, .scan appended) to sit alongside it. Individual scan payloads are decoded on demand from .wiff.scan as you iterate.

use opensxraw::reader::Reader;

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

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() {
    let spectrum = spectrum?;
    println!("{}\t{}\t{} peaks", spectrum.native_id, spectrum.ms_level, spectrum.mz.len());
}

Each yielded SpectrumRecord carries index, scan_number, native_id, ms_level, retention_time_sec, analyzer, polarity, and mz/intensity arrays. Native IDs use the PSI-MS "scan number only nativeID format" (MS:1000776): scan=N, where N is the 1-based position in the Idx stream.

  • m/z: on TripleTOF/ZenoTOF files the raw time-bin values are converted to m/z (Da) with the linear (slope, intercept) pair read from the TOFCalibrationData stream. QTRAP files carry no calibration body, so their mz values stay as raw bin values. Neither is accurate m/z: the TOF values fail physical checks (known ions, isotope spacing) and some are negative. See Known issues in the README.
  • Precursors: MS2+ spectra carry a precursor whose precursor_native_id points at the preceding MS1 scan (None if no MS1 has been seen yet). selected_mz/target_mz come from the DDERealTimeDataEx stream when present, linked by DDA cycle (a heuristic, see raw::dde); they stay None on files without that stream (for example plain SWATH or MRM).
  • Analyzer: TOFMS when a calibration body is present (TripleTOF and ZenoTOF), TQMS otherwise (QTRAP).
  • Polarity: from the sign of the ion spray voltage in the method's IonSourceParamsTable.

What the reader does not do​

  • QTRAP m/z: no clean-room calibration source is known for QTRAP files, so their mz values are raw bins.
  • Correct TOF m/z: only the first (slope, intercept) pair of TOFCalibrationData is used as a per-file constant, and the result does not match known ions in the corpus.
  • TripleTOF/ZenoTOF MS level: every scan is labelled MS2, including MS1 survey scans, so TOF MS2 spectra have no precursor m/z.
  • MRM transitions: Q1/Q3 are not exposed and no SRM chromatograms are produced.
  • Charge state and isolation window: not decoded.
  • Centroid/profile scan mode: scan_mode is left unset (None) on every spectrum. No decoded stream (Idx, DDERealTimeDataEx, SummaryInformation) carries a reliable per-scan or per-experiment centroid/profile indicator.

iter_spectra yields openmassspec_core::Result<SpectrumRecord> items. If a scan block cannot be read from the .wiff.scan file (an I/O error, or a block that starts past the end of the file), that item is an Err wrapping opensxraw::Error::ScanRead, and Reader::scan_read_failures() counts it. Iteration continues with the next scan, so a caller can stop at the first error (?) or skip and count.

Decoded per-file values​

Reader exposes what it decoded at open time through accessor methods: idx_records() (scan index: offset, size, retention time, MS level, instrument TIC), calibration(), dde_records(), instrument_info(), ion_source_parameters(), polarity(), start_timestamp(), sample() and stem(). Reader::list_samples and Reader::open_sample select one sample of a multi-sample .wiff file.

Error handling​

Public functions return opensxraw::Result<T>. The error type is opensxraw::Error, with variants Io, Parse and ScanRead. It is #[non_exhaustive], so match it with a wildcard arm. opensxraw::Error converts into openmassspec_core::Error with ? or .into(); inside the core error it is the boxed Vendor payload and can be recovered with downcast_ref::<opensxraw::Error>().