Audit Proteomics Exchange (PRIDE) study metadata from the command line.

I made PXAudit because I was checking PRIDE submissions by hand and got tired of repeating the same steps.

PXAudit reads project metadata and file listings from the PRIDE Archive, classifies the deposited files, assigns a seven-level FAIR tier and a separate quantification-readiness tier, then saves the audit to SQLite. It does not download deposited data files.

Quick start

PXAudit supports Python 3.12 through 3.14. The source checkout uses uv:

git clone https://github.com/LangeLab/PXAudit.git
cd PXAudit
uv sync
uv run pxaudit check PXD000001

The first audit queries PRIDE and creates pxaudit_results.db in the current directory. API responses are cached under ~/.pxaudit_cache/, so a fresh repeat audit does not need another request.

PXAudit currently audits PRIDE PXD accessions. Safe identifiers from other ProteomeXchange repositories are accepted as Unverifiable; repository adapters are not implemented yet.

Common tasks

# Audit a list containing one accession per line
uv run pxaudit bulk-audit --input accessions.txt --format tsv --output results.tsv

# Inspect the stored file inventory
uv run pxaudit manifest PXD000001

# Review effective settings and cache state
uv run pxaudit config show
uv run pxaudit cache info

# Generate a self-contained HTML report
uv sync --extra report
uv run pxaudit report --db pxaudit_results.db --output report/

Run uv run pxaudit --help or uv run pxaudit COMMAND --help for command-line help.

Documentation

The wiki contains the detailed contracts and examples:

• Home: workflow overview and report preview
• CLI Reference: commands, flags, configuration, caching, errors, and exit codes
• Tier System: FAIR and quantification tiers, evidence flags, and scoring rules
• Database Schema: tables, columns, migrations, and example queries
• FAQ: supported accessions, file classification, offline use, and common scoring questions
• Development: setup, architecture, testing, style, and CI

Contributions and issue reports are much appreciated. The development guide explains the local checks and documentation workflow.

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Citation

If you use PXAudit in your research, please cite it as:

@software{ergin_pxaudit_2026,
  author   = {Ergin, Enes Kemal},
  title    = {{PXAudit}: A command-line tool for auditing {Proteomics Exchange} study metadata},
  year     = {2026},
  version  = {0.5.1},
  url      = {https://github.com/LangeLab/PXAudit},
  license  = {MIT},
}

A CITATION.cff file is included in the repository root for tools that parse it automatically (e.g. GitHub's Cite this repository button, Zenodo).

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License

MIT License. See LICENSE for details.