Extended Data Figure 4:

a, Pull-down assay of HeLa cell lysate using sAB-K29. The bound proteins were separated on an SDS-PAGE gel. Gel slices were subjected to label-free quantitative mass spectrometry to identify the enriched proteins. Three biological replicates were performed. sAB-MBP was used in the control pull-down assay. Western blot analysis of the pull-down eluant using sAB-K29 or anti-ubiquitin antibody as the primary binder confirmed that sAB-MBP is an effective control. b, GO analysis (cellular components) of enriched proteins from pull-down experiments of HeLa cells using sAB-K29. The enriched proteins were identified using label-free quantitative mass spectrometry. Three biological and two technical replicates were performed. Significant hits (compared to pull down using sAB-MBP, FDR < 0.05) were subjected to GO analysis. c, Volcano plots of the quantitative mass spectrometry results. Significantly enriched hits (FDR < 0.05) are colored cyan, with some well-documented proteins involved in protein homeostasis, RNA processing, and transcription regulation highlighted and labeled.