mzdata

A Rust library for reading mass spectrometry data file formats.

Python bindings

Python bindings are available as pymzdata. Install them with:

pip install pymzdata

pymzdata provides Python 3.9+ access to mass spectrometry files through MZReader, including iteration, random spectrum access, metadata, and NumPy peak arrays. It supports mzML and indexed mzML, MGF, Bruker TDF, and imzML files. Thermo RAW files also require their native runtime dependencies. See the pymzdata README for an example and ion-mobility frame access.

Quickstart

use std::fs;
use mzdata::prelude::*;
use mzpeaks::Tolerance;
use mzdata::MzMLReader;
use mzdata::spectrum::SignalContinuity;

fn main() {
    let mut ms1_count = 0;
    let mut msn_count = 0;
    let reader = MzMLReader::open_path("./test/data/small.mzML").unwrap();
    for spectrum in reader {
        if spectrum.ms_level() == 1 {
            ms1_count += 1;
        } else {
            msn_count += 1;
        }
        println!("Scan {} => BP {}", spectrum.id(), spectrum.peaks().base_peak().mz);
        if spectrum.signal_continuity() == SignalContinuity::Centroid {
            let peak_picked = spectrum.into_centroid().unwrap();
            println!("Matches for 579.155: {:?}", peak_picked.peaks.all_peaks_for(579.155, Tolerance::Da(0.02)));
        }
    }
    println!("MS1 Count: {}\nMSn Count: {}", ms1_count, msn_count);
    assert_eq!(ms1_count, 14);
    assert_eq!(msn_count, 34);
}

Supported Formats

1. mzML and indexedmzML
2. MGF
3. mzMLb
4. Thermo RAW
5. Bruker TDF
6. imzML
7. PROXI

Disclaimer

This library was made in part to learn Rust, so it may not use the preferred idioms, patterns, or libraries. Any recommendations are welcome.