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Preprocessing and feature extraction

mzapy

Read, extract, calibrate, and visualize multidimensional mass-spectrometry data in Python, including LC-IM-MS datasets stored in MZA and selected vendor-supported formats.

LC-MSDirect-infusion MSPython packageOpen source
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Overview

mzapy is a Python package for accessing and manipulating multidimensional mass-spectrometry data. It was developed around MZA and supports data extraction, plotting, selected calibration tasks, signal processing, peak finding, and programmatic access to dimensions such as retention time, ion mobility, mass-to-charge ratio, and intensity. It is particularly useful for scripting LC-IM-MS workflows and for prototyping downstream analyses on data converted to MZA.

What can this tool do?

Chromatogram buildingPeak or feature detectionMS/MS processing

Common uses

  • Extract retention-time, ion-mobility and m/z slices from multidimensional MS datasets.
  • Build scripted LC-IM-MS analysis and visualization workflows in Python.
  • Work programmatically with MZA files generated from vendor or mzML data.

Scientific fit

Primary function

Preprocessing and feature extraction

Other functions

Data conversion and import, Visualization and reporting

MS level

MS1, MS/MS

Acquisition

Full-scan MS, Data-dependent acquisition (DDA), Data-independent acquisition (DIA)

Ion mobility

Ion mobility supported

Data compatibility

Inputs

Raw instrument data, Mass spectra

Outputs

Mass spectra, Feature or peak table

Input formats

HDF5, Other, MZA

Output formats

CSV or TSV, Other

Scope and considerations

Designed for

  • Programmatic access and lightweight analysis of multidimensional MS data, especially ion-mobility datasets.

Not designed for

  • Complete untargeted feature processing or metabolite identification by itself.

Important requirements

  • A compatible Python environment and supported input data such as MZA.

Considerations

  • Ion-mobility workflows require appropriate calibration and interpretation of the mobility dimension; extraction utilities do not by themselves establish metabolite identity.

Access and documentation

Primary accessDocumentation

mzapy is distributed as open-source Python software; current installation and dependency details are documented in the project documentation.

License: BSD-3-Clause

Evidence and review

Added from the 2026 computational-metabolomics review population and Springer methods coverage; functionality checked against the official PNNL repository, documentation and primary publication on 10 September 2026.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Ross DH, Bilbao A, Lee JY, Zheng X. mzapy: An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format. Anal Chem. 2023;95:9428-9431. doi:10.1021/acs.analchem.3c01653

Related tools

asariSimilar function · Process high-resolution mass-spectrometry data into aligned feature tables.AutoCCSSimilar function · An open-source Python tool for calculating and calibrating experimental collision cross sections from ion-mobility mass-spectrometry data across drift-tube and traveling-wave workflows.BreathXplorerSimilar function · breathXplorer processes high-resolution breath mass-spectrometry data with feature extraction, alignment and breath-recognition functions.CAMERASimilar function · Group and annotate related LC-MS signals after XCMS peak detection.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-09-10 · Entry update

    Complete mzapy editorial fields and citation

    View change · Entry at this revision
  2. 2026-09-10 · First committed entry

    Add mzapy multidimensional MS entry

    View change · Entry at this revision

Full GitHub history