pymzdata

pymzdata provides Python bindings for mzdata, a fast Rust library for reading mass spectrometry data files.

Supported formats

MZReader supports mzML and indexed mzML, MGF, Bruker TDF, and imzML files. IMMZReader provides ion-mobility frame access for compatible mzML and Bruker TDF files. Thermo RAW is also supported when its native runtime dependencies are available on the host system.

Installation

pip install pymzdata

Python 3.9 or later is required. NumPy is installed automatically and is used for the peak arrays returned by the reader.

Quickstart

import pymzdata

with pymzdata.MZReader("example.mzML") as reader:
    print(f"{len(reader)} spectra")

    for spectrum in reader:
        print(spectrum.id, spectrum.ms_level, spectrum.start_time)
        mz = spectrum.mz_array()
        intensity = spectrum.intensity_array()
        if mz is not None:
            print(f"  {len(mz)} peaks")

MZReader supports iteration and random access with get_by_index, get_by_id, and get_by_time (retention time in minutes). Spectrum metadata, precursor information, and decoded NumPy peak arrays are available from each Spectrum.

For Bruker ion-mobility data, use IMMZReader directly or convert an open MZReader with into_frame_reader() to access ion-mobility frames.

Development

To build the bindings from a checkout, install maturin and run:

cd crates/pymzdata
maturin develop