(A) Histogram showing the number of targets obtained per bait for ACAPseq with neonatal mouse brain polyribosomes for the 77/92 baits that had one or more targets. The bins represent 1 – 10, 11 – 20, 21 – 30, etc. targets. The 16 baits with zero targets are not shown. The target threshold was set at (1)>35 captured TPMs, (2) captured TPMs > 3 x the maximal number of TPMs captured with any of the other baits used in the same experimental cohort, and (3) captured TPMs > 3 x the starting TPMs in unselected polyribosomes. (B) Histograms showing the number of bait-target pairs with the corresponding values for (1) the fold enrichment of the bait-captured TPMs compared to the starting polysomes, (2) the minimum ratio of the captured TPMs for the bait of interest compared to the captured TPMs for each of the other baits in the same batch, and (3) the ratio of the captured TPMs for the bait of interest compared to the average captured TPMs for each of the other baits in the same batch. (C) Venn diagrams showing shared and unshared targets for ACAPseq [with targets that meet the threshold as defined in (A) above] and the PPIs listed in the BioGRID and IntAct databases. For BioGRID, the shared interactions are: JAM3-JAM2, EPHA4-EFNA1, EPHA3-EFNA1, PTPRZ1-CNTN1, CELSR1-LYPD6, CELSR2-LYPD6, NOTCH1-CNTN1, FLRT1-LPHN3. For IntAct, the shared interactions are: JAM3-JAM2, EPHA4-EFNA1, EPHA7-EFNA1, APP-CNTN3, PTPRZ1-CNTN1, ADGRL3-FLRT2, ADGRL3-FLRT3, UNC5B-FLRT3.