Extended Data Fig. 9: Identification of substrates of the polyubiquitination pathway by quantitative isobaric tag-based proteomics.

a, Proteins from wild-type (WT) S. cerevisiae cells, or cells expressing a Pex10 mutant defective in polyubiquitination (R324A) under the endogenous promoter, were subjected to isobaric tag-based proteomics using mass spectrometric analysis. Results are representative of two independent experiments. Each dot in the volcano plot represents a protein for which the ratio of its abundance in the R324A mutant and in wild-type cells (R324A/WT) is given, as well as a measure of statistical significance (p-value). The statistics was performed by Multiple Unpaired t-test followed by the method of Two-Stage Step-up (Benjamini, Krieger, and Yekutieli, Desired FDR (Q) = 1%) based on three biological replicates. Proteins indicated by red dots in the upper rectangle significantly accumulate in the mutant strain (P < 0.03 and R324A/WT >1.3). b, List of the proteins indicated as red dots in a. Peroxisomal proteins are highlighted with a red background. The other listed proteins are probably indirectly affected by the Pex10 mutation or erroneously identified (they include mitochondrial ribosomal proteins, cell wall proteins, and DNA binding proteins).