Figure 6.

Quantile-Quantile plot of bait vs. control marginal inclusion probabilities in the CTNNBIP1 AP-MS bait Experiment. Note the increase in quantiles in the bait compared to the control experiment as the method progresses through the procedural stages, denoted by the initial “Naïve” stage (“N”), the “Reproducible” stage (“R”), and the final “Specific” stage (“S”). This corresponds to a separation of bait versus control distributions with an accumulation towards 1 in the bait $\left({{\widehat{p}}^{\prime }}_{\text{M}}^B(j,0.75)\to 1\right)$ vs. towards 0 in the control $\left({{\widehat{p}}^{\prime }}_{\text{M}}^C(j,0.75)\to 0\right)$. Results are reported for $C_S>{\widehat{C}}_S^{\mathit{cutoff}}=0.15$ and the marginal inclusion probability thresholds ${\tilde{p}}_{\text{min}}^C=0.75$ and ${\tilde{p}}_{\text{min}}^B=0.75$.