toolGitHubJuly 2, 2026
OpenProteo: vendor-neutral Rust/Python readers for MS proteomics raw data
OpenProteo is an open-source Rust library (with Python bindings and a CLI) that reads proprietary mass-spectrometry raw formats from Thermo, Bruker, and Waters instruments and converts them into standard mzML, without requiring vendor SDKs or Windows-only DLLs. It's an umbrella project pairing with sibling crates OpenTimsTDF (Bruker timsTOF) and OpenWRaw (Waters MassLynx).
OpenProteo removes a long-standing friction point in proteomics: proprietary, vendor-locked raw file formats. It offers a unified, pure-Rust API across Thermo/Bruker/Waters raw data, converts to PSI-MS mzML, and streams into Apache Arrow for downstream analytics.
- Unified reader for Thermo, Bruker, Waters raw formats
- No proprietary SDK/DLL dependency — pure Rust
- mzML 1.1.0 conversion + Arrow streaming
- Rust library, Python package, and CLI
- Companion crates: OpenTimsTDF (Bruker .tdf), OpenWRaw (Waters .raw)