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Workflow Families

Support is evaluated separately for dda, dia, lfq, multiplex, ptm, and targeted. Each family has different source material, scientific assumptions, executable lanes, failure modes, comparison rules, and downstream consequences. Evidence from one family does not raise another family’s status.

Current Family Status

The trust status below is the strongest language defended by the checked benchmark package and black-box Runtime evidence. It is a ceiling, not a promise that every dataset inside the family will meet the same result.

family trust status primary run mode benchmark coverage current blockers
dda review_grade_bounded import_only MaxQuant primary package, Comet/Sage companion pressure, reviewed PSM/FDR/inference outputs no repository-owned raw search execution; imported engines and parameters bound parity
dia outsider_auditable_bounded raw_executable over checked reports Spectronaut primary package, DIA-NN matrix-shift companion, library-aware QC and comparison no chromatogram-native replay; library completeness and absent-peptide consequences remain bounded
lfq outsider_auditable_bounded raw_executable over checked features cohort primary package, sparse-contrast companion, normalization and missingness pressure cohort transfer and external truth beyond repeatability remain bounded
multiplex internal_support_only raw_executable over checked features TMTpro primary package, channel-stress companion, ratio and interference surfaces transfer is fragile; outsider review and laboratory consequence are not closed
ptm outsider_auditable_bounded raw_executable over checked localization inputs localization primary package, ambiguity companion, site mapping and site-level review function, occupancy, and regulatory consequence remain weaker than localization
targeted outsider_auditable_bounded raw_executable over checked targeted QC transition primary package, carryover companion, panel and follow-up records vendor parity, calibration transfer, matrix interference, and assay burden remain bounded

raw_executable means the repository can execute its declared transformation from the checked scientific inputs. It does not mean vendor-native raw files are processed for every family. import_only means the strongest lane begins with results produced by an external engine and preserves their provenance through owned review contracts. Neither mode is an accuracy grade.

Evidence Ladder

flowchart LR
    asset["source, license, and benchmark manifest"] --> science["family scientific contract"]
    science --> execution["Runtime lane and run bundle"]
    execution --> grounding["support, contradiction, and context"]
    grounding --> judgment["challenge, sensitivity, and refusal"]
    judgment --> consequence["feasibility and observed outcome"]
    consequence --> status["bounded trust status"]
    asset -. missing .-> narrow["narrow or refuse"]
    execution -. imported or unstable .-> narrow
    grounding -. contradicted .-> narrow
    consequence -. infeasible .-> narrow

The weakest required layer determines the public claim. A complete Runtime bundle cannot compensate for an unclear scientific acceptance policy. A grounded claim cannot compensate for a recommendation that reverses under a small policy change. A recommendation cannot compensate for infeasible or uninformative laboratory follow-up.

Resolve One Family Verdict

A family verdict is a join across independently reviewable records, not an average of reassuring signals. Start with the requested public language and walk left to right. At the first failed or missing contract, stop and lower the language to the strongest posture that the remaining evidence supports.

review question record that answers it narrowing condition
Can the source be identified and rebuilt? package manifest, citation manifest, generated boundary unknown source identity, prohibited redistribution, or irreproducible selection
Does the scientific contract match the family? family invariants, acceptance sheet, warning demonstrations acceptance criteria omit a family-defining failure mode
Can the declared lane be rerun? run bundle, execution mode, artifact inventory missing inputs, unstable artifacts, or an imported lane presented as native execution
Does the conclusion survive a harder package? companion package and cross_package_generalization.json direction, coverage, or acceptance changes under declared transfer pressure
Is the claim grounded at its stated strength? support, contradiction, context, and citation records contradiction is hidden or contextual evidence is promoted to direct support
Is the proposed action proportionate? challenge, refusal, feasibility, and outcome records small policy changes reverse the decision or follow-up burden defeats its value

The exact status token belongs in machine-readable evidence and in public prose. Translating it into a friendlier but stronger phrase creates a second, unreviewed release policy.

DDA

DDA support covers governed search-result intake, PSM normalization, target-decoy FDR, protein inference, quantification, and downstream review. The primary and companion lanes import external-engine results; they do not run a search engine from raw spectra inside this repository.

Inspect DDA Benchmark Lineage, DDA Cross-Package Handbook, and the Runtime Execution Boundary before making a rerun or parity claim.

DIA

DIA support covers library-conditioned precursor and protein matrices, quantification, run QC, replay, and comparison between checked Spectronaut and DIA-NN exports. The executable lane operates on those checked reports; it does not establish chromatogram-native or universal vendor parity.

Inspect DIA Benchmark Lineage and record spectral-library coverage, absent-precursor policy, and matrix-shift sensitivity with the result.

LFQ

LFQ conclusions depend on design, normalization, missingness, batch structure, aggregation, and contrast policy. The primary cohort and sparse companion give real transfer pressure, but operational repeatability is not external quantitative truth.

Inspect LFQ Benchmark Lineage and preserve the design and missingness policy alongside every comparison.

Multiplex

Multiplex has substantive scientific models and executable primary and channel-stress lanes. Its status remains internal because companion pressure exposes fragile transfer and the outsider-facing decision and laboratory chain is incomplete.

Inspect Multiplex Benchmark Lineage and Why Multiplex Stops At Internal Support. Do not borrow trust from LFQ or targeted workflows merely because their quantitative vocabulary overlaps.

PTM

PTM support separates modified-peptide evidence, localization, protein-site mapping, site-level FDR, abundance correction, motifs, occupancy, and interpretation. A confidently localized site is not automatically functional, causal, occupied, or regulatory.

Inspect PTM Benchmark Lineage and retain ambiguity and protein-abundance context through the handoff.

Targeted

Targeted support covers candidate peptides, transitions, calibration, interference, assay QC, and discovery-to-validation handoff. Matrix, calibration range, carryover, limits, transition identity, and readiness state remain part of the claim.

Inspect Targeted Benchmark Lineage before treating a technically executable follow-up as analytically transferable.

Follow A Family