DIA Benchmark Lineage

The dia 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: DIA library review public benchmark package
• public dataset identity: tracked Spectronaut-style and DIA-NN-style exported-result snapshots with explicit library-conditioned settings and confrontation scope
• dataset locator: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/package_manifest.json
• evidence tier: external_reproduction_package
• primary package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package
• companion package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package
• cross-package generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/cross_package_generalization.json

Raw Source Trail

primary flagship package

• Spectronaut DIA report snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapter_corpora/spectronaut/spectronaut_report.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/primary/spectronaut_report.tsv
• checksum: 60b2d626e92541abbd2462a293117af63829cc0c96a41077fa9408dfac3609df
• public reference: https://biognosys.com/software/spectronaut/
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh
• DIA-NN comparator export snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapter_corpora/diann/diann_pipeline_export.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/comparator/diann_pipeline_export.tsv
• checksum: 4d8e06e9ac5f9d57e861c70e47199149d5cdaddf1738bd90026d463672c9a9d6
• public reference: https://github.com/vdemichev/DiaNN
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh

companion generalization package

• DIA-NN companion report snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapters/diann_report.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/primary/diann_report.tsv
• checksum: 14e14b95d9cf889f0d2cf847a2fce4666942c51c65ef19d6192a0fd8d09fc3b5
• public reference: https://github.com/vdemichev/DiaNN
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.workflow_generalization_assets refresh
• Spectronaut companion comparator snapshot copies packages/bijux-proteomics-core/tests/fixtures/search_adapters/spectronaut_pipeline_export.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/comparator/spectronaut_pipeline_export.tsv
• checksum: fa4407b18e7c004a0c96fb0e72544c0c142007acc4fcdb4ccb13bf201e4b6068
• public reference: https://biognosys.com/software/spectronaut/
• 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/dia_library_review_package/package_manifest.json
• primary artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/artifact_inventory.json
• primary quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/quality_sheet.json
• companion package manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/package_manifest.json
• companion artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/artifact_inventory.json
• companion quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/quality_sheet.json
• family drift report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/cross_package_generalization.json

What This Lineage Does And Does Not Prove

• primary claim scope: Flagship public DIA library review package keeps dia review grounded in packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package rather than abstract benchmark prose.
• companion claim scope: Companion public DIA matrix-shift review package exists to show where dia 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.