Table 2.

Identification of Indicator Prey Proteins ${\widehat{\mathit{Q}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathbf{C}}\right)$, ${\widehat{\mathit{Q}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathbf{min}}^{\mathit{B}}\right)$ and Reproducible Experimental Replicates ${\widehat{\mathit{L}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$, ${\widehat{\mathit{L}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)$, and joint inclusion probabilities ${\widehat{\mathit{p}}}_{\mathit{\text{J}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$, ${\widehat{\mathit{p}}}_{\mathbf{\text{J}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\text{min}}^{\mathit{B}}\right)$ for a range of marginal inclusion probability thresholds ${\tilde{\mathit{p}}}_{\text{min}}^{\mathit{C}}\mathit{\in }\left[\mathbf{0},1\right]$ and ${\tilde{\mathit{p}}}_{\text{min}}^{\mathit{B}}\mathit{\in }\left[0,1\right]$ in the control and CTNNBIP1 bait experiments respectively

${\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}$Marginal Inclusion Probability Threshold	${\widehat{\mathit{Q}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$ # Selected Indicator Prey Proteins (% of ${\widehat{\mathit{\hspace{0.17em}Q}}}^{\mathit{C}}$)	${\widehat{\mathit{L}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$ # Reproducible Experimental Replicates (% of ${\mathit{K}}^{\mathit{C}}\mathbf{=}\mathbf{200}$)	${\widehat{\mathit{p}}}_{\text{J}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$ Joint Inclusion Probability	${\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}$ Marginal Inclusion Probability Threshold	${\widehat{\mathit{Q}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)$ # Selected Indicator Prey Proteins (% of ${\widehat{\mathit{\hspace{0.17em}Q}}}^{\mathit{B}}$)	${\widehat{\mathit{L}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)$ Reproducible Experimental Replicates (% of ${\mathbf{K}}^{\mathbf{B}}\mathbf{=}\mathbf{9}$)	${\widehat{\mathit{p}}}_{\mathit{\text{J}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)$ Joint Inclusion Probability
1.00	0 (0.0%)	200 (100.0%)	1.000	1.00	8 (7.5%)	9 (100.0%)	1.000
0.95	2 (0.4%)	191 (95.5%)	0.926	0.95	8 (7.5%)	9 (100.0%)	1.000
0.90	2 (0.4%)	191 (95.5%)	0.926	0.90	8 (7.5%)	9 (100.0%)	1.000
0.85	2 (0.4%)	191 (95.5%)	0.926	0.85	9 (8.4%)	8 (88.9%)	0.889
0.80	2 (0.4%)	191 (95.5%)	0.926	0.80	9 (8.4%)	8 (88.9%)	0.889
0.75	4 (0.7%)	124 (62.0%)	0.549	0.75	11 (10.3%)	5 (55.6%)	0.538
0.70	6 (1.1%)	94 (47.0%)	0.305	0.70	11 (10.3%)	5 (55.6%)	0.538
0.65	6 (1.1%)	94 (47.0%)	0.305	0.65	16 (15.0%)	2 (22.2%)	0.071
0.60	7 (1.3%)	70 (35.0%)	0.195	0.60	16 (15.0%)	2 (22.2%)	0.071
0.55	9 (1.7%)	35 (17.5%)	0.063	0.55	20 (18.7%)	2 (22.2%)	0.007
0.50	12 (2.2%)	23 (11.5%)	0.009	0.50	20 (18.7%)	2 (22.2%)	0.007
0.45	14 (2.6%)	18 (9.0%)	0.002	0.45	20 (18.7%)	2 (22.2%)	0.007
0.40	14 (2.6%)	18 (9.0%)	0.002	0.40	26 (24.3%)	0 (0.0%)	0.000
0.35	20 (3.7%)	3 (1.5%)	0.000	0.35	26 (24.3%)	0 (0.0%)	0.000
0.30	25 (4.6%)	0 (0.0%)	0.000	0.30	35 (32.7%)	0 (0.0%)	0.000
0.25	30 (5.5%)	0 (0.0%)	0.000	0.25	35 (32.7%)	0 (0.0%)	0.000
0.20	34 (6.3%)	0 (0.0%)	0.000	0.20	49 (45.8%)	0 (0.0%)	0.000
0.15	43 (7.9%)	0 (0.0%)	0.000	0.15	49 (45.8%)	0 (0.0%)	0.000
0.10	59 (10.9%)	0 (0.0%)	0.000	0.10	107 (100.0%)	0 (0.0%)	0.000
0.05	91 (16.8%)	0 (0.0%)	0.000	0.05	107 (100.0%)	0 (0.0%)	0.000
0.00	542 (100.0%)	0 (0.0%)	0.000	0.00	107 (100.0%)	0 (0.0%)	0.000

Text in italic represents the prohibited choices for the marginal inclusion probability thresholds ${\widehat{p}}_{\text{J}}^C\left({\tilde{p}}_{\text{min}}^C\right)$ and ${\widehat{p}}_{\text{J}}^B\left({\tilde{p}}_{\text{min}}^B\right)$ (see equation (4)), and bold texts represent the choices ${\tilde{p}}_{\text{min}}^C=0.75$ and ${\tilde{p}}_{\text{min}}^B=0.75$.