OpenARaw
Part of the OpenMassSpec stack for mass spectrometry raw-file access.
Rust and Python reader for Agilent MassHunter .d mass spectrometry data
directories, with no Agilent SDK or software dependency. Covers the
modern AcqData MassHunter shape across Q-TOF (profile and centroid)
and QQQ (MRM) acquisitions.
Documentation: sigilweaver.app/openaraw/docs
Known issues and gaps
- Q-TOF m/z accuracy depends on the run's calibration. The reader
applies each scan's stored calibration and does no reference-mass
correction of its own. Measured on public corpus runs: peptide fragment
ions (y1, immonium) read at a median of -2 to -9 ppm (95th percentile
8 to 16 ppm), and background ions not used for locking (siloxanes,
DEHP) at a median of -3.6 to +3.2 ppm over 19 bundles. Runs without
reference-mass correction can be off by 10 to 20 ppm:
- PXD031927 (G6550A): reference ion +12.5 ppm, siloxanes +17 to +19 ppm.
- PXD044639 (G6550B, acquisition software 10.1): purine 121.0509 at -17.5 to -19.2 ppm.
- PXD057471 (G6540A,
DefaultMassCal.xmlonly): DEHP at -11 to -13.5 ppm.
- Stored MS2 precursor m/z can disagree with the MS1 peak. In PXD031402 and PXD014285 the precursor target m/z differs from the matching MS1 peak by about 32 ppm and 10 ppm. Use a precursor tolerance of at least 30 ppm, or re-pick the precursor from the MS1 scan. Q-TOF MS2 spectra have no parent-scan link, charge state or isolation width.
- Triple quadrupole (MRM) spectra report only the product m/z. The
precursor m/z is not set and per-transition SRM chromatograms are not
emitted; each spectrum carries its MRM channel number
(
precursor_native_id = "mrm_channel=N"). Product m/z values are stored directly and match the method's transitions. - Bundles that cannot be decoded raise errors. A Q-TOF bundle with
neither
MSMassCal.binnorDefaultMassCal.xmlhas no calibration (PXD031771/655_2.d), and a bundle whose scan records point into a missing data file cannot be read (PXD022473/M.d, noMSProfile.bin). Each affected scan is an error fromiter_spectra(RuntimeErrorin Python); flight times are never reported as m/z. Malformed folders withoutAcqDataorMSScan.binfail to open (6 of 338 corpus uploads). - Corpus gaps. Tested instruments are the G6410A triple quadrupole
and G6530, G6540 and G6550 Q-TOFs. Negative mode is covered only by
the short negative segment of five PXD031771 runs (190 spectra). Not
covered: ion mobility (6560), GC-MS ChemStation
.Dfolders (DATA.MS), and models not yet seen in public data (for example 6545, 6546, 6470 and 6495).
Install
Prefer openmassspec-io
with the agilent 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 agilent
pip install openmassspec[agilent]
Standalone:
Rust:
cargo add openaraw
Python:
pip install openaraw
Quickstart
Rust:
use openaraw::reader::Reader;
use openmassspec_core::SpectrumSource;
let mut reader = Reader::open("sample.d")?;
for spectrum in reader.iter_spectra() {
let spectrum = spectrum?;
println!("{}: {} peaks", spectrum.native_id, spectrum.mz.len());
}
Python:
import openaraw
reader = openaraw.RawReader("sample.d")
spectrum = reader.read_spectrum(0)
print(spectrum.ms_level, spectrum.retention_time_sec, len(spectrum.mz))
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 accessions). See CORPUS.md and ATTRIBUTION.md.
1 maintainer
Metadata
1 maintainer
Release files for openaraw 1.0.0
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| openaraw-1.0.0.tar.gz | 63.9 kB | Details |
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