Tier System

Tier System

FAIR ladder

PXAudit scores each dataset on a 7-tier FAIR ladder. Every tier adds one requirement to the previous; a dataset must meet all criteria up to and including the tier it claims.

Tier	Requirements
None	Missing a mandatory metadata field (title, organism, or instrument)
Raw	Mandatory metadata present; no processed result files found
Bronze	Result/search files present, but none are PSI-standard (mzIdentML / mzTab)
Silver	PSI-standard results present; no SDRF experimental-design file
Gold	SDRF present; open spectra (mzML / MGF) or organism-part annotation missing
Platinum	Open spectra + organism-part annotation present; no linked PubMed publication
Diamond	All FAIR criteria met: PSI results, SDRF, open spectra, organism part, publication

Tier logic is version-stamped (tier_logic_version = "v2.0") and stored in the database so you can tell when re-scoring is needed after a logic update.

Quant tier

The quant tier is independent of the FAIR ladder. It measures how ready a dataset is for quantitative analysis.

Quant Tier	Meaning
Unverifiable	Non-PRIDE accession; cannot be evaluated
No Quant	No PSI-standard results and no tabular quant files
Partial	Either PSI-standard IDs or a quant table, but not both
Quant-Ready	PSI IDs + tabular quant table present; CV-term metadata missing
Quant-Complete	PSI IDs + tabular quant table + CV-term method metadata

Non-PRIDE accessions

Accessions from MassIVE (MSV), jPOST (JPST), and iProX (IPX) are accepted but get Unverifiable on both scores with all flags set to False. PXAudit only talks to the PRIDE API, so it can't inspect data from other repositories.

Flag inventory

These Boolean flags are computed for every PRIDE accession:

• Project-level flags

  • has_title: non-empty title present
  • has_organism: organism name present (first entry in the organisms list)
  • has_organism_id: taxonomy accession present (recorded but not used in tier gating)
  • has_instrument: instrument name present (first entry)
  • has_organism_part: tissue or cell type annotated
  • has_publication: PubMed ID linked and non-zero
  • has_quant_metadata: quantification methods described via CV terms

• File-level flags

  • has_result_files: FileClass RESULT or SEARCH files found
  • has_psi_results: FileClass RESULT (mzIdentML or mzTab)
  • has_open_spectra: FileClass PEAK (mzML, MGF, etc.)
  • has_sdrf: SDRF experimental-design file detected (PRIDE category + filename regex)
  • has_mztab: .mzTab extension found
  • has_tabular_quant: FileClass QUANT_MATRIX or ID_LIST found