Provides scope, calibration and stability diagnostics to assess
false discovery rate (FDR) claims in peptide and protein identification
workflows based on target-decoy competition and related confidence
measures. Includes the recomputed decoy ratio of the reported list,
accepted decoy counts and local decoy support, the FDP-CV benchmark,
threshold elasticity, posterior error probability (PEP) concordance with
the decoys, equal-chance checks and p-value calibration, explicit
target/decoy label-propagation rules for grouped units, picked-protein
competition, external validation by entrapment (raw and size-corrected
estimates, scope-discordant-set error rate), a ground-truth simulator of
target-decoy competition, and an HTML report. Methods are described in
Chion et al. (2026)