Fig. 3: Some RPs rapidly incorporate into neuronal ribosomes.

a Schematic of the experimental design for measuring new RPs in assembled ribosomes from cultured neurons. Normal medium was replaced by medium containing heavy amino acids (dynamic SILAC) as indicated (gray boxes). Mature ribosomes were purified by sucrose cushion. New ribosomal proteins were quantified by mass spectrometry, measuring the heavy and light peak of each peptide. b Heatmap showing for each RP the fraction of new proteins (H/(H + L)) incorporated into assembled ribosomes. Pseudocells (median of peptides obtained per individual protein) are ordered according to unsupervised clustering, both for columns (biological replicate of each condition) and rows (individual ribosomal protein). Experimental conditions of the labeling are indicated at the bottom. c, d Scatterplots showing the fraction of new RPs (H/(H + L)) in assembled ribosomes after the different labeling conditions, as indicated by x- and y-axes. Points represent average ± standard deviation of three biological replicates. Proteins are colored according to clusters identified in Fig. 3b. Some RPs of interest are indicated by name. Dashed line represents x = y. Source data are provided as a Source Data file. e, f Average ± standard deviation of the fraction of new proteins in assembled ribosomes of RPs of the same cluster, as identified in Fig. 3b. The different labeling conditions are indicated on the x-axis. Cluster A, n = 3 RPs. Cluster B, n = 4 RPs. Cluster C, n = 5 RPs. Cluster D, n = 11 RPs. Cluster E, n = 26 RPs. Cluster F, n = 21 RPs.