mzdata

A Rust library for reading mass spectrometry data file formats.

Quickstart

use std::fs::File;
use mzdata::io::prelude::*;
use mzdata::spectrum;
use mzdata::MassErrorType;
use mzdata::io::MzMLReader;

let reader = MzMLReader::new(File::open("./test/data/small.mzML").unwrap());
for spectrum in reader {
    println!("Scan ID: {} => {} data points", spectrum.id(), spectrum.mzs().len());
    for scan in iter {
        println!("Scan {} => BP {}", scan.id(), scan.peaks().base_peak().1);
        if scan.signal_continuity() < SignalContinuity::Profile {
            let peak_picked = scan.into_centroid().unwrap();
            println!("Matches for 579.155: {:?}", peak_picked.peaks.all_peaks_for(579.155, 0.02, MassErrorType::Exact));
        }
    }
}

Supported Formats

1. mzML and indexedmzML
2. MGF

TODO

1. mzML Implementation
   1. Interpret file-level metadata (file description, software, instrument configuration, data processing).
   2. Improve indexing performance, with the ability to store the computed index.
   3. Improve unit handling.
2. Iteration behavior
   1. Implement a batch iterator to group together related MS1 and MSN spectra.
   2. Implement a caching strategy for re-using recently yielded spectra.
3. Other formats?

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.