OpenProteo
Read Thermo, Bruker, and Waters data in Rust and Python.
OpenProteo is the open-source Rust stack for proteomics raw-file access. Read acquisitions from three vendor formats through a single API, convert to PSI-MS mzML 1.1.0, and stream into Arrow for downstream analytics. No vendor SDKs, no Windows-only DLLs.
Docs
API reference, quickstart, and format guides.
Source
Apache-2.0 on GitHub.
PyPI
Install with pip install openproteo.
crates.io
The openproteo-io Rust
crate.
The stack
OpenProteo is an umbrella over three vendor-specific parsers, each reverse-engineered without the vendor SDK:
-
OpenTFRaw
- Thermo Fisher
.rawfiles, format versions 8-66, from the LCQ Classic through the Orbitrap Astral. -
OpenTimsTDF
- Bruker timsTOF
.d/bundles, SQLite metadata + binary frames, LZF and zstd codecs. -
OpenWRaw
- Waters MassLynx
.rawdirectories, header, function inventory, index, chromatograms, and frame data.
Conversion
The vendor2mzml CLI
converts any supported acquisition to PSI-MS mzML 1.1.0 with a single
command. Pre-built binaries for Linux, macOS, and Windows ship with
every release. The same logic is available from Python via the
openproteo metapackage
and from Rust via the
openproteo-io crate.