mzmlpy

A lightweight Python library for parsing mzML mass spectrometry files. Initially built from pymzml, it implements a more straightforward, type-safe API and includes direct support for modern mzML structures (> 1.1.0).

Installation

pip install mzmlpy

Quick Start

from mzmlpy import Mzml

with Mzml("tests/data/example.mzML.gz") as reader:
    print(f"File ID: {reader.id}")
    print(f"Total Spectra: {len(reader.spectra)}")

    for spectrum in reader.spectra:
        print(f"Scan {spectrum.id} (MS{spectrum.ms_level}) - TIC: {spectrum.TIC}")

The Mzml reader lazily loads data, meaning binary arrays and metadata are only parsed when you access them. It supports .mzML and .mzML.gz files, and exposes spectra and chromatograms via lookup objects that support iteration, integer indexing, slicing, and string-based ID lookup.

Features

• Lazy parsing -- binary data is decoded only when accessed.
• Type-safe API -- dataclass-based models with full type annotations.
• Flexible access -- look up spectra and chromatograms by index, slice, or string ID.
• Ion mobility support -- detect and retrieve IM binary arrays.
• Comprehensive compression -- zlib, zstd, and MS-Numpress decoders built in.
• Context manager -- use with for safe file handling.

Next Steps

• Getting Started -- installation details, basic usage patterns, and working with binary data.
• API Reference -- full auto-generated documentation for every public class and method.