Multiplex Benchmark Lineage

The multiplex 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: Multiplex TMTpro public benchmark package
• public dataset identity: tracked TMTpro feature and design snapshots with explicit reporter-channel, imbalance, and missing-channel pressure
• dataset locator: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/package_manifest.json
• evidence tier: external_reproduction_package
• primary package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package
• companion package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package
• cross-package generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/cross_package_generalization.json

Raw Source Trail

primary flagship package

• TMTpro multiplex feature table snapshot copies packages/bijux-proteomics-core/tests/fixtures/quant/multiplex_ms1_features.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/evidence/multiplex_ms1_features.tsv
• checksum: 54ef1f14ff94f9bbfdb4430e940b641ac3d6c31e13d3f71c8566c5dd1b63f48b
• public reference: https://www.thermofisher.com/order/catalog/product/A44520
• rebuild command: uv run --group dev python -m bijux_proteomics.benchmarks.flagship_asset_maintenance refresh

companion generalization package

• Channel-stress multiplex feature snapshot copies packages/bijux-proteomics-core/tests/fixtures/quant/multiplex_ms1_features.tsv into packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/evidence/multiplex_channel_stress_ms1_features.tsv
• checksum: 90ae2afd5143403218c04d40c8976c3ffa2fefa0833ea99c65cff7bdf7d1271c
• public reference: https://github.com/bijux/bijux-proteomics
• 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/multiplex_tmtpro_review_package/package_manifest.json
• primary artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/artifact_inventory.json
• primary quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/quality_sheet.json
• companion package manifest: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/package_manifest.json
• companion artifact inventory: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/artifact_inventory.json
• companion quality sheet: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/quality_sheet.json
• family drift report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/cross_package_generalization.json

What This Lineage Does And Does Not Prove

• primary claim scope: Flagship public multiplex TMTpro review package keeps multiplex review grounded in packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package rather than abstract benchmark prose.
• companion claim scope: Companion public multiplex channel-stress review package exists to show where multiplex 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.