Raw Versus Import Execution

This page makes the execution-mode boundary explicit for each flagship workflow family. It exists to stop import-backed or library-conditioned lanes from quietly inheriting stronger raw-rerun language.

Why This Distinction Matters

• execution mode is one of the easiest places for docs to overstate what the repository really proves
• a lane can be useful, reviewable, and still not deserve raw-native or vendor-parity language
• this page keeps runtime honesty separate from benchmark strength and downstream recommendation strength

workflow family	current run mode	raw rerun supported	imported dependency count
dda	import_only	no	3
dia	raw_executable	yes	5
lfq	raw_executable	yes	3
multiplex	raw_executable	yes	2
ptm	raw_executable	yes	2
targeted	raw_executable	yes	4

Family Boundaries

dda

• mode difference: dda currently reruns through imported exported-result evidence instead of a raw in-repository execution lane.
• imported dependencies: packages/bijux-proteomics-core/tests/fixtures/search_adapter_corpora/maxquant/maxquant_pipeline_export.tsv, packages/bijux-proteomics-core/tests/fixtures/search_adapter_corpora/maxquant/maxquant_evidence.tsv, packages/bijux-proteomics-core/tests/fixtures/search_adapter_corpora/maxquant/maxquant_settings.txt
• blocked claims: raw external-engine parity, vendor-native or engine-native reproducibility
• claim guard: dda must not be described as raw-executable while dda-maxquant-pipeline-corpus still runs in import_only mode.

dia

• mode difference: dia executes inside the runtime package, but its benchmark package can still include imported or derived evidence that does not prove vendor-native parity.
• imported dependencies: 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
• blocked claims: chromatogram-native DIA authority, broad vendor-parity DIA replay
• claim guard: DIA remains raw-executable in runtime terms, but the shipped package still stops short of chromatogram-native and vendor-parity claims.

lfq

• mode difference: lfq executes inside the runtime package, but its benchmark package can still include imported or derived evidence that does not prove vendor-native parity.
• imported dependencies: 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
• blocked claims: none
• claim guard: lfq should keep its stronger sentence behind the current benchmark package and downstream consequence limits.

multiplex

• mode difference: multiplex executes inside the runtime package, but its benchmark package can still include imported or derived evidence that does not prove vendor-native parity.
• imported dependencies: 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
• blocked claims: outsider-auditable multiplex trust
• claim guard: Multiplex may rerun in runtime terms while still failing the stronger outsider-facing claim boundary.

ptm

• mode difference: ptm executes inside the runtime package, but its benchmark package can still include imported or derived evidence that does not prove vendor-native parity.
• imported dependencies: 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
• blocked claims: none
• claim guard: ptm should keep its stronger sentence behind the current benchmark package and downstream consequence limits.

targeted

• mode difference: targeted executes inside the runtime package, but its benchmark package can still include imported or derived evidence that does not prove vendor-native parity.
• imported dependencies: 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
• blocked claims: none
• claim guard: targeted should keep its stronger sentence behind the current benchmark package and downstream consequence limits.

What raw_executable Still Does Not Mean

• it does not mean vendor-parity authority by itself
• it does not mean companion-package transfer pressure disappeared
• it does not mean downstream lab consequence is already justified