Skip to main content

Why pure Rust

Vendor mass-spectrometry SDKs - Thermo's RawFileReader.dll, Bruker's libtimsdata, Waters' DACServer - have shaped MS tooling for two decades, but they bring real costs:

  1. Platform lock-in. Thermo ships a .NET assembly that runs only under Mono/Wine on non-Windows hosts; Waters' DAC layer is a Windows-only COM server; Bruker ships closed-source binaries with per-platform builds that lag.
  2. Auditability. Anything emitted by a closed-source reader is a black box. For regulated environments (FDA-21 CFR Part 11 records, clinical pipelines), every binary in the data path is a compliance surface.
  3. Performance. The vendor SDKs were not designed for streaming. Several materialize whole frames in memory; some force a process per file.
  4. License risk. Each SDK ships under a vendor EULA that restricts redistribution, reverse engineering, and (in some cases) benchmarking publication.

OpenProteo's pure-Rust readers address each of these:

  • Single static binary. vendor2mzml is one executable per platform with no external runtime dependencies (no .NET, no Wine, no SQLite client lib - SQLite is vendored statically by rusqlite).
  • Audit-friendly. Every line of vendor parsing is in the open under Apache-2.0. unsafe_code = "forbid" is enforced workspace- wide.
  • Streaming first. Every reader implements SpectrumSource, yielding spectra as an iterator.
  • Permissive license. Apache-2.0 across the stack. No vendor redistribution requirements.

Trade-offs​

  • We lag vendor releases. A new firmware that introduces new TDF columns requires a real change to opentimstdf, not a free pickup from a vendor update.
  • No proprietary acceleration. Where Thermo's reader can call into native FFT / centroiding, OpenProteo does the work in safe Rust. For most pipelines the difference is invisible; for raw-data hot paths it can matter.
  • Less battle-tested on exotic files. The vendor SDKs have been hit with every weird acquisition ever made. OpenProteo has a growing - but smaller - corpus. The conformance harness catches most regressions; please open an issue if you find a file we mis- parse.