opensxraw 0.2.1

Python bindings for the OpenSXRaw SCIEX .wiff / .wiff.scan file parser

OpenSXRaw

Part of the OpenMassSpec stack for mass spectrometry raw-file access. Sibling readers: OpenTFRaw (Thermo), OpenWRaw (Waters), OpenTimsTDF (Bruker), OpenARaw (Agilent).

Rust and Python reader for SCIEX .wiff/.wiff.scan legacy mass spectrometry data files, clean-room reverse-engineered with no SCIEX SDK or software dependency. Covers the TripleTOF and QTRAP instrument families.

Status

Published on crates.io (opensxraw). Python bindings (opensxraw on PyPI) publish from the release workflow. The legacy .wiff/.wiff.scan format is fully decoded and has a working reader (crates/opensxraw), tested against a real TripleTOF 5600 corpus file (2228 scans decoded).

.wiff2, SCIEX's newer self-contained format, was investigated in depth (see docs/format/03-wiff2-container.md) but uses proprietary, non-standard encryption that could not be resolved from the ciphertext alone, so .wiff2 support is deferred pending new information. See docs/format/ for the full format writeups.

Known limitations: m/z values are raw, uncalibrated time-bin integers (no ExperimentTOF calibration yet); MS2 precursor m/z is not yet populated (DDERealTimeDataEx not yet decoded). See CHANGELOG.md for the full list.

Install

Prefer openmassspec-io with the sciex feature unless you need this parser standalone (minimal dependencies, or building your own abstraction) - the umbrella gives you format auto-detection, mzML conversion, and Arrow streaming across all wired-in vendors for free:

cargo add openmassspec-io --features sciex

pip install openmassspec[sciex]

Standalone:

Rust:

cargo add opensxraw

Python:

pip install opensxraw

Quickstart

Rust:

use opensxraw::reader::Reader;
use openmassspec_core::SpectrumSource;

let mut reader = Reader::open("sample.wiff")?;
for spectrum in reader.iter_spectra() {
    println!("{}: {} peaks", spectrum.native_id, spectrum.mz.len());
}

Python:

import opensxraw

reader = opensxraw.RawReader("sample.wiff")
spectrum = reader.read_spectrum(0)
print(spectrum.ms_level, spectrum.retention_time_sec, len(spectrum.mz))

Reader::open (and RawReader) expects the paired .wiff.scan file to sit alongside the .wiff file, with .scan appended to the .wiff filename.

License

Apache-2.0. See LICENSE.

The format specification was developed by binary analysis of public mass-spectrometry datasets (PRIDE accessions). See CORPUS.md and ATTRIBUTION.md.