Benchmark Flagship Status

This page re-evaluates which public benchmark roots still deserve flagship naming. The promotion gate requires complete asset audit coverage, rebuild discipline, licensing story, comparability notes, and rerun-kit coverage before a root may keep flagship in its durable designation.

Reference surfaces:

• docs/04-bijux-proteomics-core/foundation/benchmark-licensing-and-redistribution.md
• docs/04-bijux-proteomics-core/foundation/benchmark-incompleteness-ledger.md
• docs/09-bijux-proteomics-runtime/benchmark-rerun-kits.md
• docs/09-bijux-proteomics-runtime/benchmark-comparability-matrix.md

workflow family	package role	designation	eligible
dda	primary flagship package	flagship_primary_outsider_auditable	yes
dda	companion generalization package	generalization_companion	yes
dia	primary flagship package	flagship_primary_outsider_auditable	yes
dia	companion generalization package	generalization_companion	yes
lfq	primary flagship package	flagship_primary_outsider_auditable	yes
lfq	companion generalization package	generalization_companion	yes
multiplex	primary flagship package	flagship_primary_internal_support	yes
multiplex	companion generalization package	generalization_companion	yes
ptm	primary flagship package	flagship_primary_outsider_auditable	yes
ptm	companion generalization package	generalization_companion	yes
targeted	primary flagship package	flagship_primary_outsider_auditable	yes
targeted	companion generalization package	generalization_companion	yes

Current Review

dda: primary flagship package

• package id: flagship_public_package:dda_reviewable_run
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run
• designation: flagship_primary_outsider_auditable
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• no in-repo live-engine rerun parity

• one-run package cannot authorize broad production-cohort DDA claims

dda: companion generalization package

• package id: public_companion_package:dda_cross_engine_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package
• designation: generalization_companion
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• Companion roots remain published, but their durable role is cross-package challenge rather than flagship naming.

• no live-engine rerun parity
• generalization remains bounded to two small exported-result packages

dia: primary flagship package

• package id: flagship_public_package:dia_library_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package
• designation: flagship_primary_outsider_auditable
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• no chromatogram-level vendor parity

• library incompleteness and absent-peptide consequences still block broader biological confidence

dia: companion generalization package

• package id: public_companion_package:dia_matrix_shift_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package
• designation: generalization_companion
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• Companion roots remain published, but their durable role is cross-package challenge rather than flagship naming.

• protein-evidence transfer remains weaker than precursor-level review transfer
• library-conditioned authority still caps the family posture

lfq: primary flagship package

• package id: flagship_public_package:lfq_cohort_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package
• designation: flagship_primary_outsider_auditable
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• no stronger public truth package for accuracy beyond repeatability

• generalization beyond the current cohort package remains explicitly bounded

lfq: companion generalization package

• package id: public_companion_package:lfq_sparse_contrast_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package
• designation: generalization_companion
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• Companion roots remain published, but their durable role is cross-package challenge rather than flagship naming.

• effect-direction confidence weakens under sparser contrast
• family authority remains bounded rather than decision-grade

multiplex: primary flagship package

• package id: flagship_public_package:multiplex_tmtpro_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package
• designation: flagship_primary_internal_support
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• Multiplex remains flagship-visible but internal-support only because public workflow language is intentionally narrower.

• no multiplex lab packet or outsider decision brief family
• multiplex authority is intentionally kept out of the outsider-facing flagship set

multiplex: companion generalization package

• package id: public_companion_package:multiplex_channel_stress_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package
• designation: generalization_companion
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• Companion roots remain published, but their durable role is cross-package challenge rather than flagship naming.

• Multiplex remains flagship-visible but internal-support only because public workflow language is intentionally narrower.
• multiplex still lacks outsider review and lab consequence posture
• public release language remains internal-support only even with a second package

ptm: primary flagship package

• package id: flagship_public_package:ptm_localization_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package
• designation: flagship_primary_outsider_auditable
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• occupancy and regulatory interpretation still remain narrower than localization evidence

• PTM follow-up remains exploratory and bounded by ambiguity-aware consequence planning

ptm: companion generalization package

• package id: public_companion_package:ptm_ambiguity_stress_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package
• designation: generalization_companion
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• Companion roots remain published, but their durable role is cross-package challenge rather than flagship naming.

• targetability weakens materially under ambiguity stress
• family authority remains bounded rather than decision-grade

targeted: primary flagship package

• package id: flagship_public_package:targeted_transition_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package
• designation: flagship_primary_outsider_auditable
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• vendor-parity and calibration-clean authority are still outside the current proof boundary

• targeted follow-up remains exploratory and cannot authorize calibration-perfect biological certainty

targeted: companion generalization package

• package id: public_companion_package:targeted_carryover_review_package
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package
• designation: generalization_companion
• asset audit complete: yes
• rebuild path complete: yes
• licensing story complete: yes
• comparability complete: yes
• rerun kit complete: yes

• eligible for designation: yes

• Companion roots remain published, but their durable role is cross-package challenge rather than flagship naming.

• stronger carryover pressure weakens promotion confidence
• family authority remains bounded by calibration and vendor-parity limits