OpenWRaw
Part of the OpenMassSpec stack for mass spectrometry raw-file access.
Rust and Python reader for the Waters MassLynx RAW mass spectrometry data format. Cross-platform (Linux, macOS, Windows), with no native or system dependencies.
Documentation: sigilweaver.app/openwraw/docs
Install
Prefer openmassspec-io
with the waters feature/extra 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 waters
pip install openmassspec[waters]
Standalone:
Rust:
cargo add openwraw
Python:
pip install openwraw
Quickstart
Rust:
use openwraw::Reader;
let r = Reader::open("sample.raw")?;
for f in &r.functions {
println!("function {}: {} scans", f.index, f.scan_count());
}
Python:
import openwraw
r = openwraw.RawReader("sample.raw")
spec = r.read_spectrum(1, 0)
print(spec.mz[:5], spec.intensity[:5])
See the docs site for the full quickstart, guide, and format specification.
Known issues and gaps
- m/z is not lock-mass corrected, and is typically 30 to 100 ppm off.
m/z uses only the calibration stored in
_HEADER.TXT. Lock-mass (reference) functions are skipped when iterating spectra and are not used to correct the others. Measured on the 69 lock-mass functions of the public test corpus, the reference ion reads about 46 ppm from its true m/z (median), 98 ppm at the 95th percentile and up to 162 ppm. For accurate-mass work, recalibrate against known masses (most search engines have a mass recalibration step; the bundle's own lock-mass scans are available throughReader::decode_scan), or search with tolerances of at least 100 ppm. - No ion mobility decoding. SYNAPT, Vion and Cyclic IMS scans are returned as m/z and intensity only. There is no drift-time output, and mzML output carries no mobility arrays.
- DDA precursors carry m/z only. Data-dependent MS/MS scans report the precursor m/z recorded for each scan, as both isolation window target and selected ion m/z. No charge state, isolation width or reference to the triggering survey scan is reported; none has been found in the files.
- MS level of Vion MSe data. The high-energy function of an MSe
acquisition is reported as MS2 when the bundle labels it
TOF PARENT, or labels itTOF MSand records its collision-energy ramp. Vion bundles exported by UNIFI record no collision energy, so both of theirTOF MSfunctions are reported as MS1. - Polarity is reported only when the bundle records it. UNIFI exports do not, so their spectra have no polarity.
- Encoding E (12-byte records): intensity flag bits and the auxiliary word are not interpreted; flagged peaks are kept. Encoding E spectra are labelled centroid. That is confirmed from point spacing for the Xevo G2-XS lock-mass functions but not for LCT Premier bundles.
- Tested instruments. The public test corpus covers Q-Tof, SYNAPT, Vion, Cyclic IMS and Xevo G2-XS/G3 QTof data in positive mode, including MSe, HDMSe, DDA, targeted MS/MS and one MALDI MS/MS bundle. Triple and single quadrupole (MRM/SIR), GC and negative-mode data are untested.
Debug logging
OpenWRaw logs how it reads a bundle: which side files it resolved
(including sample-prefixed names), instrument and geometry from
_extern.inf, and for each function the scan count, mass range, chosen
record encoding and why, and calibration. Warnings flag skipped functions,
missing calibration, unreadable _FUNCnnn.STS files, and indexes that
address more bytes than their DAT file holds. Per-scan byte ranges are
logged at trace level.
Rust uses the log facade; install any logger:
RUST_LOG=openwraw=debug your-program sample.raw # with env_logger
Python forwards to the standard logging module under the openwraw
logger. Configure it before opening files:
import logging
logging.basicConfig(level=logging.DEBUG)
import openwraw
openwraw.RawReader("sample.raw")
Include this output when reporting a file that fails to open or decode.
Corpus decode audit
Run every non-lock-mass scan in a directory tree of Waters RAW bundles:
cargo run -p openwraw --release --example audit_corpus -- /path/to/corpus
The command reports opened bundles, decoded scans, and the first error per
bundle, then checks each lock-mass function against its reference compound
(ReferenceMass1 in _extern.inf, or Leu-Enk / Glu-fib). It exits with an
error if any bundle fails to open, any scan fails to decode, or any lock-mass
function is more than 100 ppm off. Add --lock-only to skip the full scan
pass.
The 2026-09-26 corpus audit records the expanded corpus results and the format gaps it exposed.
Repository layout
crates/
openwraw/ Core Rust library
openwraw-py/ PyO3 / maturin Python bindings
docs/ Docusaurus site (format spec + guides)
License
Apache-2.0. See LICENSE.
The format specification was developed by binary analysis of public mass-spectrometry datasets (PRIDE accessions). See ATTRIBUTION.md.
1 maintainer
Metadata
1 maintainer
Release files for openwraw 4.0.0
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| openwraw-4.0.0.tar.gz | 78.6 kB | Details |
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