Supplementary Figure 6: PUP-IT^MUL1 and PUP-IT^RNF13 identify unique interacting proteins.

(a) Cellular localization of MUL1-PafA and RNF13-PafA. HeLa cells were transfected with either MUL1-PafA-myc or RNF13-PafA-myc, then cells were fixed and stained with anti-myc antibody. This experiment was repeated independently twice with similar results. (b) Volcano plot of PUP-IT^MUL1 and PUP-IT^CD28. The logarithmic ratios of protein LFQ-intensity (CD28/MUL1) was plotted against negative logarithmic P value of a two-sided two samples t-test in Perseus. Mitochondria located proteins, including RHOT1, TOM70 and HK2 are uniquely identified in PUP-IT^MUL1 datasets (Supplementary Table 3b). (c) Volcano plot of PUP-IT^MUL1 and PUP-IT^RNF13. The logarithmic ratios of protein LFQ-intensity (RNF13/MUL1) was plotted against negative logarithmic P value of a two-sided two samples t-test in Perseus. Ubiquitin ligase RNF13 uniquely binds the ubiquitin conjugating enzyme UBE2H (Supplementary Table 3c). In (b) and (c), the green and blue dots represent significantly enriched proteins from common hits (FDR ≤ 0.05, n = 3 independent experiments).