FAQ

What accessions can PXAudit audit?

Any PRIDE accession (prefix PXD). Accessions from MassIVE (MSV), jPOST (JPST), and iProX (IPX) are accepted but score Unverifiable. PXAudit only has access to the PRIDE REST API.

Does PXAudit download my data files?

No. It only queries metadata endpoints. No raw data, result files, or anything else gets downloaded.

How are files classified?

Three-stage deterministic pipeline:

1. Extension registry: maps known extensions like .mzML, .raw, .mzid to a FileClass
2. Exact-stem map: catches MaxQuant fixed filenames like proteinGroups.txt
3. Regex patterns: matches tool-specific output names like report.tsv, psm.tsv

The PRIDE fileCategory tag is used only as a fallback when none of the above match. Compression suffixes (.gz, .zip, .bz2) are stripped before classification so results.mzid.gz classifies the same as results.mzid.

Why is my dataset scoring lower than expected?

A few common reasons:

• Missing metadata: title, organism, or instrument absent. Result: None.
• No result files: the submission has raw data but nothing processed. Result: Raw.
• Non-standard results: only proprietary search output, no mzIdentML or mzTab. Result: Bronze.
• No SDRF: no experimental-design file. Result: Silver.
• Partial submission: PARTIAL submissions have relaxed requirements but may still lack files.

How can I re-score datasets after a logic update?

Check which accessions used an older version of the tier logic:

SELECT accession FROM audit WHERE tier_logic_version != 'v2.0';

Then re-run pxaudit check on those accessions to update their scores.

Does PXAudit work offline?

Partially. Once an accession has been audited, its raw API responses are cached under ~/.pxaudit_cache/. Subsequent runs reuse the cache. If the network is down and stale cached data exists, PXAudit falls back to it with a warning.

What is the cache TTL?

Default is 7 days. Use --refresh to force a re-fetch regardless of cache age.

How do I cite PXAudit?

@software{ergin_pxaudit_2026,
  author   = {Ergin, Enes Kemal},
  title    = {{PXAudit}: A command-line tool for auditing {Proteomics Exchange} study metadata},
  year     = {2026},
  version  = {0.3.0},
  url      = {https://github.com/LangeLab/PXAudit},
  license  = {MIT},
}