MetaX

MetaX is a novel tool for linking peptide sequences with taxonomic and functional information in Metaproteomics. We introduce the Operational Taxon-Function (OTF) concept to explore microbial roles and interactions ("who is doing what and how") within ecosystems.

MetaX also features statistical modules and plotting tools for analyzing peptides, taxa, functions, proteins, and taxon-function contributions across groups.

📥Download MetaX

Operational Taxon-Function (OTF)

Operational Taxon-Function (OTF) Unit: An operational unit which represents the association between specific taxa and biological functions.

OTF Analyzer

The Tools in OTF Analyzer

OTF Examples

Linking Taxa and Functions in different levels of the hierarchy, and various functional categories. e.g., Species-KO, Genus-CAZy, Phylum-EC, etc. Lots of visualization tools can be selected.

Network

Dots represent taxa and squares represent functions in the network.

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Heatmap

Show all Taxa of a function.

• 

Bar

Show all functions of a taxon

• 

OTF Heatmap

Show OTFS intensity in groups(samples), e.g., Species-KO OTF Heatmap

Download & Installation

• Desktop Version (Recommended)

  The desktop version comes fully set up and ready to use, including all required dependencies and a graphical user interface.

  Download the MetaX Desktop Version

• Lightweight annotation CLI

  The default PyPI installation contains the OTF annotation backend and CLI without Qt:

  python -m pip install MetaXTools

  Run annotation with the same Python environment that installed MetaX:

  python -m metax.cli.annotate --config annotation.yaml

• Headless Analyzer and Report

  Install the Analyzer without Qt, or install the complete headless Report stack:

  python -m pip install "MetaXTools[analyzer]"
  python -m pip install "MetaXTools[report]"
  metax-report --config report.yaml

• Desktop GUI / complete installation

  The desktop profile includes Analyzer, statistics, plotting, Report, notebook export, and Qt:

  python -m pip install "MetaXTools[full]"
  metax

  If an optional stack is missing, metax and metax-report exit with a clear message identifying the required extra.

Guidebook

• Desktop Version(desktop):
  • Refer to the MetaX Cookbook for detailed instructions on how to use MetaX with the graphical user interface.
  
  
• Command-line version:
  • See the MetaX CLI tab for installation profiles, peptide-to-OTF annotation, automated reports, database building, and workflow automation.
  • Read the example documentation in the Notebook for analysis examples.

Citing

If you use MetaX in your research, please cite the following publication:

Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics. Wu, Q., Ning, Z., Zhang, A., Zhang, X., Sun, Z., & Figeys, D. (2025). Analytical Chemistry. DOI: 10.1021/acs.analchem.4c06645.