Benchmark Freshness Review

This page records whether each flagship workflow family still has a current benchmark review window, whether the checked freshness report still records its copied snapshots and remote references as available, and whether a stronger checked replacement is already recorded. Release narrowing consumes these rows directly when freshness drops below the current public sentence.

Coverage

workflow family	review state	remote reference state	requested language	release language floor
dda	current	recorded_available	outsider_auditable_bounded	outsider_auditable_bounded
dia	current	recorded_available	outsider_auditable_bounded	outsider_auditable_bounded
lfq	current	recorded_available	outsider_auditable_bounded	outsider_auditable_bounded
multiplex	current	recorded_available	internal_support_only	internal_support_only
ptm	current	recorded_available	outsider_auditable_bounded	outsider_auditable_bounded
targeted	current	recorded_available	outsider_auditable_bounded	outsider_auditable_bounded

Family Review

dda

• 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
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run
• last reviewed on: 2026-05-05
• freshness window: 365 days
• freshness due on: 2027-05-05
• review state: current
• remote reference state: recorded_available
• stronger replacement recorded: no
• replacement note: No stronger checked replacement is recorded yet. Replace the one-run DDA package with a multi-run public DDA asset root that still preserves paired comparator confrontation.
• requested release language: outsider_auditable_bounded
• release language floor: outsider_auditable_bounded
• blockers: none
• evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/package_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/source_locator_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/freshness_report.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/obsolescence_audit.json

dia

• 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
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package
• last reviewed on: 2026-05-07
• freshness window: 365 days
• freshness due on: 2027-05-07
• review state: current
• remote reference state: recorded_available
• stronger replacement recorded: no
• replacement note: No stronger checked replacement is recorded yet. Replace the import-backed DIA package with a raw-executable or chromatogram-backed DIA asset root.
• requested release language: outsider_auditable_bounded
• release language floor: outsider_auditable_bounded
• blockers: none
• evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/package_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/source_locator_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/freshness_report.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/obsolescence_audit.json

lfq

• benchmark title: LFQ cohort review public benchmark package
• public dataset identity: tracked study-scale feature and cohort-design snapshots with explicit missingness and repeatability boundaries
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package
• last reviewed on: 2026-05-07
• freshness window: 365 days
• freshness due on: 2027-05-07
• review state: current
• remote reference state: recorded_available
• stronger replacement recorded: no
• replacement note: No stronger checked replacement is recorded yet. Replace the current LFQ package with a pair of public cohort packages that expose stronger truth and generalization pressure.
• requested release language: outsider_auditable_bounded
• release language floor: outsider_auditable_bounded
• blockers: none
• evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/package_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/source_locator_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/freshness_report.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/obsolescence_audit.json

multiplex

• 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
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package
• last reviewed on: 2026-05-07
• freshness window: 365 days
• freshness due on: 2027-05-07
• review state: current
• remote reference state: recorded_available
• stronger replacement recorded: no
• replacement note: No stronger checked replacement is recorded yet. Replace the current TMTpro package with a broader multiplex asset root that includes runtime and follow-up consequence closure.
• requested release language: internal_support_only
• release language floor: internal_support_only
• blockers: none
• evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/package_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/source_locator_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/freshness_report.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/obsolescence_audit.json

ptm

• benchmark title: PTM localization public benchmark package
• public dataset identity: tracked localization, PTM feature, raw-spectrum, and sequence-context snapshots with explicit ambiguity limits
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package
• last reviewed on: 2026-05-07
• freshness window: 365 days
• freshness due on: 2027-05-07
• review state: current
• remote reference state: recorded_available
• stronger replacement recorded: no
• replacement note: No stronger checked replacement is recorded yet. Replace the current PTM package with one that broadens PTM-family scope and closes runtime plus comparator gaps.
• requested release language: outsider_auditable_bounded
• release language floor: outsider_auditable_bounded
• blockers: none
• evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/package_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/source_locator_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/freshness_report.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/obsolescence_audit.json

targeted

• benchmark title: Targeted transition public benchmark package
• public dataset identity: tracked chromatogram-shaped QC table plus approved, failed, and refused follow-up packet snapshots
• package root: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package
• last reviewed on: 2026-05-07
• freshness window: 365 days
• freshness due on: 2027-05-07
• review state: current
• remote reference state: recorded_available
• stronger replacement recorded: no
• replacement note: No stronger checked replacement is recorded yet. Replace the current targeted package with a raw-executable targeted asset root that includes calibration and comparator closure.
• requested release language: outsider_auditable_bounded
• release language floor: outsider_auditable_bounded
• blockers: none
• evidence paths: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/package_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/source_locator_manifest.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/freshness_report.json, packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/obsolescence_audit.json