Figure 8.

FDR computed from SAINT posterior probability output (${\mathit{P}}_{\mathit{SAINT}}$) as a function of procedural stages: from the initial “Naïve” stage (“N” – SAINT-only), to the “Reproducible” stage (“R”), and to the final “Specific” stage (“S” – ROCS-SAINT) in the CTNNBIP1 (left) and STK24 (right) AP-MS bait experiment. Results are reported for $C_S>{\widehat{C}}_S^{\mathit{cutoff}}$ and the marginal inclusion probability thresholds ${\tilde{p}}_{\text{min}}^C$ and ${\tilde{p}}_{\text{min}}^B$ as determined in each AP-MS experiment (see Tables 1 and 3).