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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() {
    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, and mz/intensity arrays. For MS2+ scans, precursor is populated with a placeholder native-ID reference rather than a real precursor m/z (SCIEX's Idx stream does not store precursor m/z; it lives in the not-yet-decoded DDERealTimeDataEx stream) - see Format specification for where that data actually lives on disk.

What the reader does not yet do​

  • m/z calibration: mz values are the raw time-bin integer read directly from the token stream, not a calibrated Da value. Real calibration requires the ExperimentTOF method-stream constants, not yet decoded.
  • Precursor m/z: as above, MS2 spectra don't carry a real target_mz yet.
  • Instrument-aware scan mode: every spectrum is currently reported as profile-mode with a TOFMS analyzer, regardless of whether the source file is actually a QTRAP acquisition (which is nominal-mass, not true time-of-flight). This is a simplification in the current reader, not a property of the format itself.

Error handling​

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