mzdata 0.66.0

A library to read mass spectrometry data formats and a data model for mass spectra
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# mzdata

[![Latest Version](https://img.shields.io/crates/v/mzdata?style=for-the-badge&color=mediumpurple&logo=rust)](https://crates.io/crates/mzdata)
[![docs.rs](https://img.shields.io/docsrs/mzdata?style=for-the-badge&logo=docs.rs&color=mediumseagreen)](https://docs.rs/mzdata/latest/mzdata/)

A Rust library for reading mass spectrometry data file formats.

## Python bindings


Python bindings are available as [pymzdata](https://pypi.org/project/pymzdata/).
Install them with:

```console
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](crates/pymzdata/README.md) for an example and ion-mobility frame
access.

## Quickstart

```rust
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.