Fig. 7: Selectivity of ER-phagy receptors in ER remodelling in iNeurons revealed by combinatorial multiplexed proteomics.
From: Combinatorial selective ER-phagy remodels the ER during neurogenesis
a, Scheme depicting an 18-plex TMT experiment examining the total proteomes of the indicated single ER-phagy receptor mutant day-12 iNeurons. Violin plots (lower panel) depicting log2FC (mutant/WT) for the indicated classes of ER proteins in single-mutant iNeurons (day 12) are shown in the lower plot. b, Scheme depicting an 18-plex TMT experiment examining the total proteomes of the indicated combinatorial ER-phagy receptor mutant day-12 iNeurons. Violin plots (lower panel) depicting log2FC (mutant/WT) for the indicated classes of ER proteins in combinatorial mutant iNeurons (day 12) are shown in the lower plot. c, log2FC (mutant/WT) distributions of ER proteins compared to randomized selections of the same number of proteins (100 iterations). P values for each comparison are calculated with a Kolmogorov–Smirnov test (two-sided). d, Application of a linear model to identify selective cargo for individual ER-phagy receptors via quantitative proteomics. In the linear model, a coefficient FC (β) is calculated for sequential loss of ER-phagy receptors starting from WT to DKO, then DKO to TKO, then TKO to QKO, then QKO to PKO. e, β coefficient values (top panel) and log2FC (lower panel) for FAM134A. The green asterisk in the top panel indicates a significant change (adjusted P value of <0.05) in the β coefficient for that mutant. P values for β values extracted from the linear model are calculated with a Student’s t-test (two-sided), with multiple hypothesis correction using the Benjamini–Hochberg method. This analysis is distinct from traditional comparisons between each mutant and WT (lower panel). f, Violin plots depicting the β coefficient FC for the indicated classes of ER proteins. P values for each comparison are calculated with a one-sided Wilcoxon test with Bonferroni correction. g, Top 25 accumulating ER proteins in WT to DKO and QKO to PKO and their respective ER compartment compared to the landscape of the whole ER. The TMT ratio check and normalization are available in the source data.
