OpenSXRaw
OpenSXRaw is one of the vendor readers in
OpenMassSpec, a Rust- and
Python-native stack for proteomics raw-file access. Sibling readers:
OpenTFRaw (Thermo .raw),
OpenWRaw (Waters .raw/),
OpenTimsTDF (Bruker .d/),
OpenARaw (Agilent .d/).
OpenSXRaw is a Rust library that reads SCIEX .wiff/.wiff.scan legacy
mass-spectrometry data files - the paired-file binary format produced by
SCIEX TripleTOF and QTRAP instruments running Analyst acquisition
software.
It runs on Linux, macOS, and Windows, with no dependency on any SCIEX SDK
or software. The format was decoded by clean-room binary analysis of a
public corpus of mass-spectrometry datasets (PRIDE accessions); see
CORPUS.md.
What it covers
| Component | Status |
|---|---|
.wiff CFBF container (method/sample metadata, Idx stream) | supported |
.wiff.scan block index and token-stream decoding | supported |
| TripleTOF instrument family | supported |
| QTRAP instrument family | supported |
.wiff2 container | not supported (encrypted, out of scope) - see Format specification |
m/z calibration (TOFCalibrationData) | TripleTOF/ZenoTOF: one linear calibration per file, m/z not accurate; QTRAP: raw bin values, not m/z |
MS2 precursor m/z (DDERealTimeDataEx) | decoded on DDA files (cycle-linked heuristic) |
CI runs the conformance suite against a public QTRAP 6500+ fixture.
TripleTOF/ZenoTOF m/z values fail physical checks (known fragment ions, background ions, isotope spacing) and some are negative; QTRAP m/z values are raw detector bins. TripleTOF/ZenoTOF files also decode with every scan labelled MS2, including survey scans. Do not use OpenSXRaw m/z values for identification or accurate-mass work. See Known issues and gaps in the README.
Next steps
- Install the Rust crate.
- Run through the Quickstart.
- Read the Format specification for the binary layer.
License
OpenSXRaw is Apache-2.0 licensed. See License.