openproteo-io 1.0.0

Vendor-neutral mass-spec I/O: feature-gated re-exports of opentfraw / opentimstdf / openwraw with auto-detection and an mzML writer.
Documentation

openproteo-io

Working name. See RENAME-TBD.md for the final-name discussion.

Umbrella of the OpenProteo stack for proteomics raw-file access. Vendor readers OpenTFRaw (Thermo), OpenTimsTDF (Bruker), and OpenWRaw (Waters) sit on top of shared core openproteo-core. Columnar storage and analysis lives in ProLance, a downstream consumer.

openproteo-io is the umbrella crate that ties together the open Rust mass-spec parsers:

Vendor Format Crate
Thermo Fisher .raw (Finnigan) opentfraw
Bruker timsTOF .d/ (TDF) opentimstdf
Waters MassLynx .raw/ bundle openwraw

It re-exports each vendor parser behind a Cargo feature, adds auto-detection of vendor format from a path, and provides a single vendor2mzml binary that converts any supported input to PSI-MS mzML 1.1.0 via the canonical writer in openproteo-core.

Crates

  • crates/openproteo-io (lib) - feature-gated vendor re-exports plus detect_format / convert_to_mzml helpers.
  • crates/openproteo-io-cli (bin vendor2mzml) - the one-stop CLI.
  • crates/openproteo-io-py (PyO3) - Python bindings exposing zero-copy NumPy views (planned).

Quick start

cargo run -p openproteo-io-cli --release -- \
    /path/to/sample.raw /tmp/sample.mzML --indexed

License

Apache-2.0. The vendor crates each carry their own license headers and upstream attribution notes; this repo only orchestrates them.