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Flagship Public Benchmark Catalog

bijux-proteomics-core publishes one explicit catalog for the flagship public benchmark packages and their companion generalization packages that downstream review, runtime, knowledge, intelligence, and lab surfaces rely on.

The point of this catalog is not volume. It is to make one reviewer ask and one answer possible:

Which public benchmark packets exist for this workflow family, what machine-readable surfaces do they expose, and what authority still stays blocked when the family is forced off its easiest package?

Reading Rule

  • treat each flagship package root as a reviewable scientific packet, not as a branded folder name
  • treat each companion package root as the first pressure test on whether the flagship sentence survives beyond its easiest benchmark
  • treat the family-transfer report as the release-language brake, not as an optional appendix

Current Catalog

dda

  • flagship 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
  • family-transfer report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/cross_package_generalization.json
  • machine-readable package surfaces: package manifest, artifact inventory, quality posture, lifecycle posture, scientific invariants, warning demonstrations

dia

  • flagship 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
  • family-transfer report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/cross_package_generalization.json
  • machine-readable package surfaces: package manifest, artifact inventory, quality posture, lifecycle posture, Spectronaut-style report, paired pipeline exports

lfq

  • flagship package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package
  • companion package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package
  • family-transfer report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/cross_package_generalization.json
  • machine-readable package surfaces: package manifest, artifact inventory, quality posture, lifecycle posture, study-scale feature table, cohort design table

multiplex

  • flagship 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
  • family-transfer report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/cross_package_generalization.json
  • machine-readable package surfaces: package manifest, artifact inventory, quality posture, lifecycle posture, reporter feature table, multiplex design table

ptm

  • flagship package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package
  • companion package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package
  • family-transfer report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/cross_package_generalization.json
  • machine-readable package surfaces: package manifest, artifact inventory, quality posture, lifecycle posture, localization table, PTM feature table, reference FASTA, raw spectra

targeted

  • flagship package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package
  • companion package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package
  • family-transfer report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package/cross_package_generalization.json
  • machine-readable package surfaces: package manifest, artifact inventory, quality posture, lifecycle posture, targeted QC table, approved follow-up packet, failed follow-up packet, refused follow-up packet

What This Catalog Guarantees

  • every flagship family has one durable package root instead of scattered proof fragments
  • every flagship family also has one companion package root and one published family-transfer report before family-level trust language is allowed
  • every package ships machine-readable package identity, artifact inventory, quality posture, and lifecycle posture
  • every package also ships source locators, citation manifests, generated boundaries, and rebuild instructions

What This Catalog Makes Easier To See

  • which workflow families now have genuinely inspectable outsider packets
  • which scientific surfaces each family exposes at package level before runtime or intelligence turns them into another narrative layer
  • why multiplex still stops at internal-support family language even though its benchmark surface is much more real than older docs admitted

What This Catalog Does Not Guarantee

  • outsider-auditable authority for every workflow family
  • live runtime execution for every package
  • comparator parity for every package
  • decision-grade scientific support across the whole catalog
  • stability across more than the current paired package story for each family

multiplex stays an internal-support family even though it already has a real pair of public packages and a raw-executable runtime lane, because its current stress packet still collapses outsider-facing trust.

Asset Maintenance

Open Flagship Benchmark Assets when you need the copied-source contract, citation discipline, refresh command, freshness report, or obsolescence audit for these package roots.

Open Flagship Challenge Corpus Catalog when you need the blinded holdouts and perturbation roots that deliberately try to break the claims these package roots would otherwise make too comfortably.

Next Routes

  • Open Workflow Families when the question becomes which family currently deserves stronger public language.
  • Open Execution when the question becomes how these package roots turn into rerun lanes and checked runtime artifacts.
  • Open Decision Support when the question becomes whether grounding, recommendation posture, or release language outruns the package story.

Boundary

This catalog should settle package identity, paired-package coverage, and the first-order transfer surface. It should not pretend that catalog presence by itself earns runtime parity, grounded scientific support, or downstream assay confidence.