Table 3 ROCS results for the number of Indicator Prey Protein s, Reproducible Experimental Replicates , and joint inclusion probability ${\widehat{p}}_{\text{J}}$ at various experimental scales K in each AP-MS control and bait experiments: STK24, PPM1B, NME2, CTNNBIP1, VHL, and CONTROL

Bait Experiment with experimental

scale K(${\mathit{K}}^{\mathit{C}}$ or${\mathit{K}}^{\mathit{B}}$)

${\widehat{\mathit{Q}}}^{\mathit{B}}$ or${\widehat{\mathit{Q}}}^{\mathit{C}}$

# Total Indicator Prey Proteins

${\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}$ or${\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}$

Bait Marginal Inclusion Probability Threshold

${\widehat{\mathit{Q}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)$ or ${\widehat{\mathit{Q}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$

# Selected Indicator Prey Proteins

(% of${\widehat{\mathit{Q}}}^{\mathit{B}}$ or${\widehat{\mathit{Q}}}^{\mathit{C}}$)

${\widehat{\mathit{L}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)$ or${\widehat{\mathit{L}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$

# Reproducible Experimental Replicates

(% of${\mathit{K}}^{\mathit{C}}$ or${\mathit{K}}^{\mathit{B}}$)

${\widehat{\mathit{p}}}_{\mathit{\text{J}}}^{\mathit{B}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{B}}\right)$ or${\widehat{\mathit{p}}}_{\mathit{\text{J}}}^{\mathit{C}}\left({\tilde{\mathit{p}}}_{\mathit{min}}^{\mathit{C}}\right)$

Joint Inclusion Probability