OpenSZRaw
Part of the OpenMassSpec stack for mass spectrometry raw-file access.
Rust and Python reader for Shimadzu LabSolutions mass spectrometry raw
data (.lcd LC-MS, .qgd GCMS, .gcd GC), with no Shimadzu SDK or
software dependency. Covers .qgd GC-MS (full-scan profile and
MRM/targeted) and .lcd LC-MS across IT-TOF (profile) and QTOF
(centroid) acquisitions.
Documentation: sigilweaver.app/openszraw/docs
Known issues and gaps
These apply to openszraw 0.3.0 and all earlier releases. Figures come from checks run on the public validation corpus (see CORPUS.md).
- LC-MS QTOF (
.lcd, LCMS-9030) m/z values are wrong. Intensities decode correctly, but the m/z axis is distorted: isotope partners of intense peaks appear about 1100/m Da apart (1.86 Da at m/z 592, 1.04 Da at m/z 1062) instead of 1.003 Da. Measured in two independent accessions; this affects all 416 QTOF files in the corpus. Do not use QTOF m/z values for identification or accurate-mass work. The error depends on m/z, so a single offset does not correct it. - LC-MS IT-TOF (
.lcd) m/z values are not validated. The per-file calibration fits the file's own tuning data, but in the files checked no isotope structure or cluster of known background ions could be found. 21 of 29 sampled files have spectra that are not sorted by m/z, and noise points map to m/z values up to about 780,000. This affects all 2,230 IT-TOF files in the corpus. Treat IT-TOF m/z as unverified. - IT-TOF MS level and polarity are not decoded. Every spectrum is
labelled MS1 with no polarity, although files carry up to 4 interleaved
acquisition channels that likely alternate polarity or MS level. Treat
ms_levelas unreliable on IT-TOF files. The channel is exposed asextra["openszraw.channel_index"], but which channel is which is not known. - LC-MS/MS triple quadrupole
.lcd(LCMS-8040/8050/8060) is not supported.Reader::openrefuses these files (275 corpus files). - Polarity is not reported for any file type.
- QTOF MS2 spectra have no precursor m/z. They link to their MS1 scan only.
- Single quadrupole
.lcd(LCMS-2020): some spectra are not sorted by m/z (all 5 sampled files, about 18 percent of spectra). - No TIC or base-peak chromatograms are produced. LC detector chromatograms are decoded only for the few files whose format is understood.
- About 0.2 percent of QTOF scans fail to decode. Each one is an
Erritem fromiter_spectra(counted byReader::skipped_scans()), so mzML export of an affected file stops there unless the writer is told to skip bad records (RecordErrorPolicy::Skip). In Python,RawReaderanditer_spectraraiseRuntimeErrorfor such a scan unless called withskip_errors=True.
What has been checked and holds:
- GC-MS
.qgd(full-scan profile and MRM): m/z is consistent with unit-resolution GC-MS (93 percent of the 5 most intense peaks per spectrum lie within 0.1 of an integer mass). Every MRM spectrum carries its precursor target m/z; the transitions have not been cross-checked against the acquisition method. Two.qgdfiles are checked in CI. - Single quadrupole
.lcd: summed intensity matches the file's own TIC stream, and m/z sits on a 0.1 grid from 400 to 2000, as expected for a unit-resolution instrument. No reference ions were available to check mass accuracy directly. - QTOF intensities: the maximum intensity of every non-empty spectrum equals the base-peak intensity the file records (150,731 of 150,731 sampled spectra). Retention times never step backwards in a 63-file sample covering every supported variant.
Install
Prefer openmassspec-io
with the shimadzu 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 shimadzu
pip install openmassspec[shimadzu]
Standalone:
Rust:
cargo add openszraw
Python:
pip install openszraw
Quickstart
Rust:
use openszraw::reader::Reader;
use openmassspec_core::SpectrumSource;
let mut reader = Reader::open("sample.lcd")?;
for spectrum in reader.iter_spectra() {
let spectrum = spectrum?;
println!("{}: {} peaks", spectrum.native_id, spectrum.mz.len());
}
Python:
import openszraw
reader = openszraw.RawReader("sample.lcd")
spectrum = reader.read_spectrum(0)
print(spectrum.ms_level, spectrum.retention_time_sec, len(spectrum.mz))
Reader::open (and RawReader) auto-detects .qgd vs .lcd IT-TOF vs
.lcd QTOF from the file's internal CFBF stream layout, never from the
filename or extension alone.
See the docs site for the full guide, format specification, and API reference.
License
Apache-2.0. See LICENSE.
The format specification was developed by binary analysis of public mass-spectrometry datasets (PRIDE, MassIVE, and MetaboLights accessions). See CORPUS.md and ATTRIBUTION.md.
Metadata
Release files for openszraw 0.3.0
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