Table 1.

ROCS results for the number of Experimental Replicates and Prey Proteins as a function of procedural stages from the initial “Naïve” stage (“N”), to the “Reproducible” stage (“R”), and to the final “Specific” stage (“S”) for all the AP-MS bait experiments: VHL, CTNNBIP1, NME2, PPM1B, and STK24

Stages	Stage “N”		Stage “R”		Stage “S”
Bait Experiment	Experimental Replicates $\left({\mathit{K}}^{\mathit{B}}\right)$	Prey Proteins $\left({\mathit{N}}^B\right)$	Reproducible Experimental Replicates $\left({\widehat{\mathit{L}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)\right)$	Reproducible Prey Proteins $\left({\mathit{R}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)\right)$	Reproducible Experimental Replicates $\left({\widehat{\mathit{L}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)\right)$	Specific Prey Proteins $\left({\mathit{S}}^{\mathit{B}}({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}},{\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}},{\mathit{C}}_{\mathit{S}}^{\mathit{cutoff}})\right)$	$\left({\widehat{\mathit{C}}}_{\mathit{S}}^{\mathit{cutoff}}\right)$
STK24	5	824	3	141	3	112	(0.13)
PPM1B	6	965	3	111	3	76	(0.08)
NME2	8	1349	8	329	8	260	(0.09)
CTNNBIP1	9	1229	5	106	5	69	(0.15)
VHL	33	5398	11	323	11	43	(0.14)

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 bait experiment.