GO term enrichment and selected brassinosteroid signaling components in IP-MS with the TRAPPII-specific CLUB:GFP subunit as bait. Light-grown inflorescences were used (see Fig. 1, B and C; Kalde et al., 2019). As control, the soluble GFP empty vector was used. Three replicates were carried out for the IP-MS experiments. (A) Gene ontology (GO) term enrichment analysis of the TRAPPII interactome. Depicted are highly abundant (fold enrichment ≥4) and significant (FDR-adjusted P value ≤0.003) GO term associations of biological processes of level 0. The length of each bar corresponds to the fold enrichment of GO terms associated with detected proteins, while the color intensity indicates the significance given as the P value adjusted for the false discovery rate (FDR). The GO term enrichment analysis was carried out with high-confidence interactors (intensity ratio >8 and P value ≤0.02; see Fig. 1 B). Note that the majority of GO terms are associated with trafficking and transport (12/30). GO terms associated with response to stimulus, light responses, and cell division were also enriched. (B) Individual intensity-based absolute quantification (iBAQ) values in log₂ scale of brassinosteroid-related proteins (highlighted in Fig. 1 C) found in each CLUB:GFP IP-MS replicate. Selected brassinosteroid-related proteins were differentially enriched over light- versus dark-grown seedlings in a different IP-MS experiment. Dots clustered at the bottom of the graphs represent peptides that were not detected (or detected as very low intensity) in the sample. P values were obtained using the Welch’s t test. Related to Fig. 1, and Table S1.