Extended Data Fig. 1. Coverage-aware definition and validation of the assayable CSF proteome.

(a) Coverage-aware detection workflow. Twenty-one informative mass-spectrometry (MS) studies were ordered by protein depth. For each index study, the assayable universe comprised observed proteins plus proteins supported by depth-matched studies within a centred three-study window. Detection tiers were assigned from the pooled lower 95% confidence bound, with proteins supported by fewer than six informative studies assigned to Tier E. (b) Assayable protein universes across the 21 derivation studies, ordered by observed depth. Blue, observed proteins; orange, proteins added by local support. (c) Correspondence between coverage-aware and coverage-naive detection-tier assignments. Tiles show protein counts and row-normalized percentages. (d) Overlap between Tier A proteins identified by CAD and CND-based approach. (e,f) Precision–recall (e) and receiver operating characteristic (f) benchmarks of CAD and CND scores against the mapped Waury et al. high-confidence CSF reference (probability ≥ 0.90; n = 12,021 proteins)¹⁴. CAD, coverage-aware detection; CND, coverage-naive detection.