openmassspec-core

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

Shared, vendor-neutral foundation for the OpenMassSpec 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/openmassspec/docs

Install

cargo add openmassspec-core

With the optional Arrow bridge:

cargo add openmassspec-core --features arrow

Quick example

Implement SpectrumSource and write a valid indexed mzML document:

use openmassspec_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 OpenMassSpec 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.