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MetaPilot v1.0.0

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@cksakura cksakura released this 19 Jun 13:50
v1.0.0
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MetaPilot v1.0.0

MetaPilot v1.0.0 is the first formal public release of MetaPilot, with release packages for both Windows desktop use and Linux/HPC command-line execution.

MetaPilot is a metaproteomics workflow platform for DDA and DIA datasets. It supports genome-aware genome selection, refined database or spectral-library construction, taxonomy export, and functional annotation reporting.

Highlights

  • First formal MetaPilot release.
  • Windows GUI release for the broadest workflow coverage.
  • Linux/HPC CLI release through metapilot-cli.
  • Shared metapilot-core workflow engine for parsing, genome selection, taxonomy, reporting, and resource handling.
  • Java 17+ based release packages.

Windows GUI

The Windows desktop application supports interactive setup and execution for the main MetaPilot workflow families:

  • DDA IGC workflows: MaxQuant, pFind, FragPipe, and Sage.
  • DDA MAG workflows: pFind, FragPipe, and Sage.
  • DIA workflows: DIA Marker, DIA Seed, DIA Target, and DIA Real-Time.
  • Resource configuration for external tools including DIA-NN, FragPipe/MSFragger, pFind, MaxQuant, Sage, DeepDetect, Python, and functional annotation resources.
  • MAG database configuration and workflow parameter loading.
  • Result folder cleaner for preview-first cleanup of workflow outputs.

Linux / HPC CLI

This release introduces the Linux command-line package for supported headless workflows.

Current headless execution supports:

  • DIA_MARKER: Core/Focus, Comprehensive, Deep together, and Deep per file.
  • DDA_MAG_FRAGPIPE: MAG-aware DDA FragPipe workflow.

The CLI includes commands for:

  • Initial site configuration.
  • Resource path setup and validation.
  • MAG database registration.
  • Parameter validation.
  • Headless workflow execution.

Example entry point:

java -jar metapilot-cli-1.0.0-shaded.jar --help

Citation

If you use MetaPilot in your work, please cite the MetaPilot preprint:

MetaPilot: genome-aware adaptive search-space refinement for unified DDA and DIA metaproteomics
bioRxiv, 2026. DOI: 10.64898/2026.06.12.728088

@article{metapilot2026,
  title = {MetaPilot: genome-aware adaptive search-space refinement for unified DDA and DIA metaproteomics},
  journal = {bioRxiv},
  year = {2026},
  doi = {10.64898/2026.06.12.728088}
}
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