Fig. 1: Quantitative mass spectrometry-based analysis of ribosome-bound Otu2 versus Ubp3.

a Scheme outlining the sample preparation for mass spectrometry. MS mass spectrometry, AP affinity purification, TCA trichloroacetic acid, TEV tobacco etch virus. b Nu-PAGE gel of affinity purified fractions by Otu2-FTpA and Ubp3-FTpA. r-proteins; ribosomal proteins. We obtained essentially the same results in at least three independent experiments. The original gel is provided in the Source data file. c Volcano plot showing the fold change (log2 LFQ Otu2-TEV/LFQ Ubp3-TEV) on the x-axis and the P-value distribution on the y-axis for the proteins identified in the affinity purifications. Missing values were imputed from a normal distribution (width, 0.3; down-shift, 1.8). To test for differentially abundant proteins, a two-sided T-test was employed. Multiple testing correction was performed with a permutation-based FDR estimation (FDR  <  0.05). q-values ≤ 0.05 with log2-fold changes < −0.6 and > 0.6 were considered as statistically significant. Each circle indicates an identified protein. Hits were grouped in categories and color coded as indicated in the panel. Gray dots represent unspecific or unrelated hits. Enriched proteins from the Otu2 purification can be found on the right side, de-enriched ones on the left side. LFQ label-free quantification, SSU and LSU small and large ribosomal subunit, ER endoplasmic reticulum. d Volcano plots as in c for wash samples after S7 nuclease treatment highlighting enriched initiation factors. Source Data for (c) and (d) are provided in the Source data file, that contains the complete inventory.