Benchmark Comparability Matrix

This matrix states how each workflow family behaves when the public sentence has to survive both the primary flagship package and the companion generalization package.

How To Read This Matrix

• read the stability score as a family-transfer stress result, not as a generic quality badge
• compare run modes and weakened claims together because one family can rerun cleanly and still lose language under companion pressure
• treat collapsed claims as the clearest signal that the public sentence must stay narrow

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

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.

What This Matrix Makes Easier To See

• why multiplex can be operationally real and still remain below outsider trust
• why stronger runtime lanes do not automatically erase weakened or collapsed claims
• which flagship families still owe their public caution to family-transfer pressure rather than to missing execution alone