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Benchmark Licensing and Redistribution

This page makes the current licensing and redistribution posture explicit for every public benchmark root. It exists so a reviewer can tell the difference between what the repository redistributes as governed evidence and what remains only a public reference or external-engine context.

Package Matrix

workflow family package role redistributed evidence count package root
dda primary flagship package 5 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run
dda companion generalization package 7 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package
dia primary flagship package 5 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package
dia companion generalization package 4 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package
lfq primary flagship package 3 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package
lfq companion generalization package 3 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package
multiplex primary flagship package 2 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package
multiplex companion generalization package 2 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package
ptm primary flagship package 4 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package
ptm companion generalization package 4 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package
targeted primary flagship package 4 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package
targeted companion generalization package 4 packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package

Licensing Stories

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
  • dataset reuse note: The tracked DDA package reuses checked-in raw-like and imported-result snapshots as governed benchmark evidence and does not imply redistribution rights for any broader external-engine dataset outside those snapshots.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/evidence/spectra.mgf
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/primary/maxquant_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/comparator/msfragger_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/evidence/design.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_reviewable_run/evidence/workflow_end_to_end_expectations.json

Current licensing limits:

  • The tracked DDA package currently ships checked exported-result snapshots, not live MaxQuant or MSFragger executables.
  • The local file is a tracked snapshot; public availability check targets the project source page, not a downloadable binary.
  • The local file is a tracked snapshot; public availability check targets the project source page, not an executable redistribution path.
  • Public availability check targets the reference resource page used by the package README and citation manifest.

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
  • dataset reuse note: The tracked DDA package reuses checked-in raw-like and imported-result snapshots as governed benchmark evidence and does not imply redistribution rights for any broader external-engine dataset outside those snapshots.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/evidence/spectra.mgf
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/evidence/design.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/evidence/workflow_end_to_end_expectations.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/primary/comet_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/primary/comet.params
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/comparator/sage_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dda_cross_engine_review_package/comparator/sage_config.json

Current licensing limits:

  • The DDA companion package ships checked exported-result and raw-like snapshots, not live Comet or Sage executables.
  • The local file is a tracked snapshot; the public check targets the project page rather than a binary download.
  • The local file is a tracked snapshot; the public check targets the documentation site.

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
  • dataset reuse note: The checked-in DIA fixture is reused as internal benchmark evidence and does not widen redistribution rights for vendor DIA outputs beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/primary/spectronaut_report.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/primary/spectronaut_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/primary/spectronaut_settings.txt
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/comparator/diann_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_library_review_package/comparator/diann_config.json

Current licensing limits:

  • The DIA package currently ships imported report snapshots and settings, not live vendor chromatogram execution.
  • The local file is a tracked snapshot; public availability check targets the product reference page.
  • The local file is a tracked snapshot; public availability check targets the public project page.

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
  • dataset reuse note: The checked-in DIA fixture is reused as internal benchmark evidence and does not widen redistribution rights for vendor DIA outputs beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/primary/diann_report.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/primary/diann_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/comparator/spectronaut_pipeline_export.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/dia_matrix_shift_review_package/comparator/spectronaut_settings.txt

Current licensing limits:

  • The DIA companion package ships checked exported-result snapshots and remains library-conditioned.
  • The local file is a tracked snapshot; the public check targets the project repository.
  • The local file is a tracked snapshot; the public check targets the product page.

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
  • dataset reuse note: The checked-in LFQ fixture is reused as internal benchmark evidence and does not widen redistribution rights for any external quantification pipelines beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/evidence/study_scale_ms1_features.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/evidence/study_scale.design.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_cohort_review_package/evidence/quant_reproducibility_manifest.json

Current licensing limits:

  • The LFQ package currently ships cohort-shaped feature and design snapshots, not a second raw cohort or spike-in truth package.
  • The local file is a tracked snapshot; public availability check targets the public methodology reference.

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
  • dataset reuse note: The checked-in LFQ fixture is reused as internal benchmark evidence and does not widen redistribution rights for any external quantification pipelines beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/evidence/edge_case_ms1_features.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/evidence/edge_case.design.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/lfq_sparse_contrast_review_package/evidence/sparse_reproducibility_manifest.json

Current licensing limits:

  • The LFQ companion package ships tracked feature and design snapshots rather than raw vendor data.
  • This tracked file is a repository-owned snapshot.

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
  • dataset reuse note: The checked-in multiplex fixture is reused as internal benchmark evidence and does not imply redistribution rights for any vendor multiplex outputs beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/evidence/multiplex_ms1_features.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_tmtpro_review_package/evidence/multiplex.design.tsv

Current licensing limits:

  • The multiplex package currently ships TMTpro-shaped feature and design snapshots, not a raw vendor acquisition replay.
  • The local file is a tracked snapshot; public availability check targets the chemistry reference page.

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
  • dataset reuse note: The checked-in multiplex fixture is reused as internal benchmark evidence and does not imply redistribution rights for any vendor multiplex outputs beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/evidence/multiplex_channel_stress_ms1_features.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/multiplex_channel_stress_review_package/evidence/multiplex_channel_stress.design.tsv

Current licensing limits:

  • The multiplex companion package ships a derived stress table rather than raw reporter-ion vendor data.
  • This tracked file is a repository-owned derived snapshot.

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
  • dataset reuse note: The checked-in PTM fixture is reused as internal benchmark evidence and does not imply redistribution rights beyond the repository’s reviewed test data.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/evidence/localization_results.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/evidence/ptm_features.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/evidence/ptm_sites.fasta
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_localization_review_package/evidence/spectra.mgf

Current licensing limits:

  • The PTM package currently ships localization and occupancy snapshots, not live rescoring or broad PTM-family execution parity.
  • The local file is a tracked snapshot; public availability check targets the PTM-localization reference page.

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
  • dataset reuse note: The checked-in PTM fixture is reused as internal benchmark evidence and does not imply redistribution rights beyond the repository’s reviewed test data.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/evidence/localization_results.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/evidence/ptm_features.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/evidence/ptm_sites.fasta
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/ptm_ambiguity_stress_review_package/evidence/spectra.mgf

Current licensing limits:

  • The PTM companion package ships tracked ambiguity-stress snapshots rather than vendor-native raw files.
  • This tracked file is a repository-owned derived snapshot.

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
  • dataset reuse note: The checked-in chromatogram fixture is reused as internal benchmark evidence and does not widen redistribution rights for vendor targeted outputs beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/evidence/targeted_benchmark_qc.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/follow_up/supported_targeted_follow_up.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/follow_up/failed_targeted_transition_follow_up.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_transition_review_package/follow_up/refused_targeted_follow_up.json

Current licensing limits:

  • The targeted package currently ships transition QC and consequence packet snapshots, not live vendor chromatogram execution or external calibration reruns.
  • The local file is a tracked snapshot; public availability check targets the targeted-guideline reference page.

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
  • dataset reuse note: The checked-in chromatogram fixture is reused as internal benchmark evidence and does not widen redistribution rights for vendor targeted outputs beyond the repository snapshot.

Redistributed evidence inside the package root:

  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package/evidence/targeted_benchmark_qc.tsv
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package/follow_up/supported_targeted_follow_up.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package/follow_up/failed_targeted_transition_follow_up.json
  • packages/bijux-proteomics-core/benchmark-assets/flagship-public-packages/targeted_carryover_review_package/follow_up/refused_targeted_follow_up.json

Current licensing limits:

  • The targeted companion package ships a derived QC table and copied follow-up packets rather than vendor-native chromatograms.
  • This tracked file is a repository-owned derived snapshot.