Ownership Boundary

Core owns deterministic proteomics computation and the scientific contracts needed to review it. Inputs, policies, accepted and rejected material, diagnostics, ambiguity, and limitations must remain visible independently of the caller or execution environment.

flowchart LR
    I["scientific inputs"] --> C["Core operation"]
    P["explicit method policy"] --> C
    C --> A["accepted results"]
    C --> X["rejections and ambiguity"]
    C --> Q["QC and limitations"]
    A --> R["Runtime execution"]
    A --> K["Knowledge grounding"]

Owned Scientific Surfaces

Surface	Core authority
formats and intake	FASTA, spectra, mzML, tables, search-engine exports, normalized bundles
sequence and chemistry	digestion, modifications, masses, fragments, target-decoy construction
identification	PSM normalization, score orientation, FDR, protein inference, ambiguity
quantification	normalization, missingness, differential analysis, protein and peptide summaries
workflow families	DDA, DIA, LFQ, multiplex, PTM, targeted scientific contracts
interpretation	enrichment and biological-context computations over explicit inputs
benchmarks	fixtures, reference cases, comparators, acceptance, challenge corpora
scientific artifacts	typed reports, QC, rejected rows, policy, provenance, limitations

Refused Ownership

Core does not own process state, providers, retries, scheduling, replay, evidence custody, citation truth, recommendation policy, laboratory readiness, or repository governance. A Core result can be executed by Runtime, grounded by Knowledge, judged by Intelligence, and acted on by Lab without transferring those authorities into the scientific operation.

Placement Test

Keep a change in Core when the same scientific inputs and policy should produce the same reviewable result regardless of process environment. Move it to Runtime when it concerns when, where, or how work executes; to Knowledge when it concerns claim support; to Intelligence when it selects or recommends; and to Lab when it concerns practical follow-up or outcomes.

Scientific convenience is not enough. A helper belongs here only when it preserves an owned scientific invariant and exposes the evidence required to challenge it.