DDA Benchmark Lineage

The dda family now has a two-root lineage instead of one convenient package story. This page ties the primary flagship package, the companion generalization package, and the cross-package drift report together so an outsider can follow the evidence chain from copied input to derived review surface.

Family Contract

• benchmark title: DDA reviewable public benchmark package
• public dataset identity: tracked raw-like spectrum plus paired MaxQuant and MSFragger exported-result snapshots inside one outsider-readable DDA package
• dataset locator: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/package_manifest.json
• evidence tier: external_reproduction_package
• primary package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run
• companion package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package
• cross-package generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/cross_package_generalization.json

Raw Source Trail

primary flagship package

• MaxQuant DDA export snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapter_corpora/maxquant/maxquant_pipeline_export.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/primary/maxquant_pipeline_export.tsv
• checksum: e4e83e3d45817dded49899f201b5933ac30dfd61355a1246f111549afc82f427
• public reference: https://www.maxquant.org/
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh
• MSFragger comparator export snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapter_corpora/msfragger/msfragger_pipeline_export.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/comparator/msfragger_pipeline_export.tsv
• checksum: fb6fbbb6d104dda343db8eb0d084904f246e477661278610346168a7db9c1e24
• public reference: https://msfragger.nesvilab.org/
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh
• UniProt reference proteome design context copies packages/bijux-proteomics-core/tests/fixtures/production_run/design.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/evidence/design.tsv
• checksum: 59a5f9786b825bca78ab9e046a07de06baf76ba484b6cd3acb3a64b0ba013c0d
• public reference: https://www.uniprot.org
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh

companion generalization package

• Comet DDA companion export snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapters/comet_pipeline_export.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/primary/comet_pipeline_export.tsv
• checksum: a6703d9c661db306f31ebe597d84a6af95f1edb4cc693476fc13ad2e85776f8e
• public reference: https://uwpr.github.io/Comet/
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.workflow_generalization_assets refresh
• Sage DDA companion comparator snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapters/sage_pipeline_export.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/comparator/sage_pipeline_export.tsv
• checksum: a8d6bdc68faf5287b4084a9ff40dfe0fd4cf4ab9c116aff5a9284051ec6039ce
• public reference: https://sage-docs.vercel.app/
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.workflow_generalization_assets refresh

Derived Review Surfaces

• primary package manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/package_manifest.json
• primary artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/artifact_inventory.json
• primary quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/quality_sheet.json
• companion package manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/package_manifest.json
• companion artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/artifact_inventory.json
• companion quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/quality_sheet.json
• family drift report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/cross_package_generalization.json

What This Lineage Does And Does Not Prove

• primary claim scope: Flagship public DDA reviewable run keeps dda review grounded in packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run rather than abstract benchmark prose.
• companion claim scope: Companion public DDA cross-engine review package exists to show where dda family transfer weakens, not to hide that drift.
• current cross-package note: This report is the public family-transfer surface. It records what still survives when the workflow moves from the flagship primary package to a second package with a materially different pressure profile.

Rebuild Order

1. Refresh the primary root with uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh.
2. Refresh the companion root with uv run --group dev python -m bijux_proteomics.benchmarks.workflow_generalization_assets refresh.
3. Re-read the family drift report before strengthening any workflow-family sentence.