Benchmark Comparability Matrix

This matrix tests whether a workflow-family statement survives both its primary flagship package and a companion package with a materially different pressure profile. It reports survival, weakening, and collapse separately so a stable aggregate score cannot conceal a failed claim.

flowchart LR
    primary["primary flagship run"] --> compare["family comparison"]
    companion["companion pressure run"] --> compare
    compare --> survive["surviving claims"]
    compare --> weaken["weakened claims"]
    compare --> collapse["collapsed claims"]
    survive --> boundary["bounded public language"]
    weaken --> boundary
    collapse --> refusal["narrow or refuse"]

Family Comparison

Workflow family	Public language	Primary run mode	Companion run mode	Stability score	Surviving claims	Weakened claims	Collapsed claims
dda	outsider_auditable_bounded	import_only	import_only	0.83	1	1	0
dia	outsider_auditable_bounded	raw_executable	raw_executable	0.83	1	1	0
lfq	outsider_auditable_bounded	raw_executable	raw_executable	0.84	1	1	0
multiplex	internal_support_only	raw_executable	raw_executable	0.7	1	0	1
ptm	outsider_auditable_bounded	raw_executable	raw_executable	0.8	1	1	0
targeted	outsider_auditable_bounded	raw_executable	raw_executable	0.87	1	1	0

Read The Matrix

• surviving means the declared claim remains supported in both packages under the recorded comparison policy;
• weakened means the direction survives but scope, certainty, or transfer language must narrow;
• collapsed means the companion evidence does not support the claim and release language must exclude it;
• the stability score summarizes the governed findings but never overrides a collapsed claim;
• run mode distinguishes native Runtime computation from custody of imported external-engine results.

Family Notes

dda

• primary 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
• generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/cross_package_generalization.json

• stability label: highly_stable

• Compare the primary MaxQuant import path against the paired MSFragger comparator export inside the tracked DDA package.

• Preserve target-decoy visibility and explicit protein-rollup caution rather than flattening DDA review into engine-agnostic certainty.
• 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.

dia

• 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
• generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/cross_package_generalization.json

• stability label: highly_stable

• Compare adapter-normalized outputs against the tracked DIA public package because direct DIA-NN or Spectronaut execution is outside repo scope.

• Keep SWATH-style transition semantics aligned with the published DIA method reference.
• 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.

lfq

• primary 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
• generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/cross_package_generalization.json

• stability label: highly_stable

• Compare rollups against the tracked LFQ public package instead of claiming parity with unexecuted external quantification pipelines.

• Keep support claims scoped to repeatable abundance aggregation and design preservation.
• 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.

multiplex

• 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
• generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/cross_package_generalization.json

• stability label: fragile_transfer

• Compare reporter handling against the tracked multiplex public package because direct vendor-specific multiplex pipelines are not executed here.

• Limit support claims to channel semantics and chemistry caveats, not full external pipeline parity.
• 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.

ptm

• primary 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
• generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/cross_package_generalization.json

• stability label: highly_stable

• Compare localization handling against the checked-in PTM localization fixture because direct rescoring engines are not executed in the repo test path.

• Retain Ascore-style ambiguity framing and PSI-MOD grounding in the resulting claims.
• 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.

targeted

• primary 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
• generalization report: packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package/cross_package_generalization.json

• stability label: highly_stable

• Compare targeted QC handling against the tracked targeted public package and published protein-inference caution rather than claiming direct vendor chromatogram parity.

• Keep support claims scoped to transition-level evidence retention and cautious rollup semantics.
• 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.

Decision Rule

A family may keep only the language that survives its primary and companion packages, their declared comparison policy, and all visible collapsed findings. Evidence from another family cannot repair a failure here.