openproteo-core

Part of the OpenProteo stack for proteomics raw-file access. Sibling readers: OpenTFRaw (Thermo), OpenTimsTDF (Bruker), OpenWRaw (Waters).

Shared, vendor-neutral foundation for the OpenProteo mass-spec stack: the SpectrumSource trait every parser implements, the canonical SpectrumRecord / RunMetadata types, a streaming mzML 1.1.0 writer (with optional indexed mzML output and SHA-1 footer), an optional Apache Arrow RecordBatch bridge, and a cross-vendor conformance harness.

MSRV: 1.85
License: Apache-2.0
#![forbid(unsafe_code)]

Documentation: sigilweaver.app/openproteo/docs

Install

cargo add openproteo-core

With the optional Arrow bridge:

cargo add openproteo-core --features arrow

Quick example

Implement SpectrumSource and write a valid indexed mzML document:

use openproteo_core::{
    write_indexed_mzml, RunMetadata, SpectrumRecord, SpectrumSource,
};

struct MySource {
    spectra: Vec<SpectrumRecord>,
}

impl SpectrumSource for MySource {
    fn run_metadata(&self) -> RunMetadata {
        RunMetadata::default()
    }
    fn iter_spectra<'a>(&'a mut self) -> Box<dyn Iterator<Item = SpectrumRecord> + 'a> {
        Box::new(self.spectra.drain(..))
    }
    fn spectrum_count(&self) -> Option<usize> {
        Some(self.spectra.len())
    }
}

let mut src = MySource { spectra: vec![/* SpectrumRecord { .. } */] };
let mut out = std::fs::File::create("run.mzML")?;
write_indexed_mzml(&mut src, &mut out)?;
# Ok::<(), Box<dyn std::error::Error>>(())

Public API

Symbol	Module	Purpose
`SpectrumRecord`	`types`	Decoded spectrum: id, ms level, polarity, rt, peaks, precursor.
`PrecursorInfo`	`types`	Selected / isolated precursor, charge, activation, scan window.
`ChromatogramRecord`	`types`	TIC / BPC / SRM trace.
`RunMetadata`	`types`	Run-level CV terms: instrument, source format, native id format.
`CvTerm`	`types`	A PSI-MS controlled-vocabulary term.
`Polarity`, `Analyzer`, `ScanMode`, `MsPower`, `Activation`	`enums`	Standard enumerations.
`MobilityArrayKind`	`enums`	Per-peak inverse-mobility / drift-time array kind.
`SpectrumSource`	`source`	Trait every parser implements.
`write_mzml`	`mzml`	Stream a `SpectrumSource` to a plain mzML 1.1.0 document.
`write_indexed_mzml`	`mzml`	Same, with `<indexList>` + SHA-1 footer for byte-offset indexing.
`conformance::assert_source_invariants`	`conformance`	Check a live `SpectrumSource` for cross-vendor invariants.
`conformance::assert_iter_invariants`	`conformance`	Same, but from any `IntoIterator<Item = SpectrumRecord>`.
`arrow::SpectrumBatchBuilder`	`arrow` (feat)	Zero-copy builder for `arrow_array::RecordBatch` from a spectrum stream.
`arrow::spectrum_record_schema`	`arrow` (feat)	The canonical Arrow schema.
`Error`	`error`	Aggregate `thiserror`-based error type.

Conformance harness

The conformance module enforces the cross-vendor invariants every parser must satisfy:

monotonic spectrum indices,
non-negative, non-decreasing retention times,
equal-length m/z and intensity arrays,
equal-length mobility arrays (when present),
MS-level / polarity sanity,
precursor presence on MSn spectra.

Failures surface as ConformanceError variants (PeakArrayLengthMismatch, MobilityArrayLengthMismatch, RetentionTimeNonMonotonic, and others).

The vendor2mzml validate subcommand in the OpenProteo umbrella runs this harness on any vendor input or pre-existing mzML.

Feature flags

Flag	Default	Effect
`arrow`	off	Enables `arrow_array::RecordBatch` building from spectra.

Changelog

See CHANGELOG.md.

License

Apache-2.0. See LICENSE.

openproteo-core 1.0.1