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Data conversion and import

MZA

Convert multidimensional mass-spectrometry data from vendor formats or mzML into an HDF5-based MZA structure for efficient storage and programmatic access.

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Overview

MZA is a stand-alone converter and data structure for multidimensional mass-spectrometry data, including LC-IM-MS and DIA datasets. It converts supported proprietary files and mzML into an HDF5-based representation designed to make large, heterogeneous MS datasets easier to access from multiple programming languages and operating systems.

What can this tool do?

MS/MS processing

Common uses

  • Convert LC-MS, LC-IM-MS and DIA datasets into a common HDF5-based representation.
  • Make multidimensional MS data accessible to Python, R and other HDF5-capable environments.

Scientific fit

Primary function

Data conversion and import

Other functions

Data management and sharing

MS level

MS1, MS/MS

Acquisition

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

Ion mobility

Ion mobility supported

Data compatibility

Inputs

Raw instrument data

Outputs

Raw instrument data

Input formats

Vendor raw format, mzML

Output formats

HDF5, MZA

Scope and considerations

Designed for

  • Data conversion and storage for large multidimensional MS datasets.

Not designed for

  • Feature detection, compound annotation or statistical interpretation by itself.

Important requirements

  • Supported vendor-format data or mzML input and the dependencies required by the selected converter.

Considerations

  • Vendor-format conversion may depend on vendor-provided libraries and licensing terms.

Access and documentation

Primary access

The repository provides source code and examples, while binary use can also depend on vendor data-access libraries and their terms.

Evidence and review

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

Core publications

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

  1. Bilbao A, et al. MZA: a data conversion tool to facilitate software development and artificial intelligence research in multidimensional mass spectrometry. J Proteome Res (2023). doi:10.1021/acs.jproteome.2c00313

Related tools

AirdProSimilar function · AirdPro converts mass-spectrometry vendor data into the Aird storage format through a graphical batch-conversion workflow.arcMSSimilar function · arcMS converts Waters UNIFI MS-E and HDMS-E data into tabular Parquet or HDF5 storage for analysis in R or Python.MobilityTransformRSimilar function · MobilityTransformR converts CE-MS migration times to an effective-mobility scale using added mobility markers.msconvertSimilar function · Convert mass-spectrometry files into open formats for downstream analysis.

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 MZA editorial fields

    View change · Entry at this revision
  2. 2026-09-10 · Entry update

    Fix MZA YAML citation quoting

    View change · Entry at this revision
  3. 2026-09-10 · First committed entry

    Add MZA data-conversion entry

    View change · Entry at this revision

Full GitHub history