Cell samples were lysed in lysis buffer (8 M urea, 1% protease inhibitor cocktail). The supernatant was collected and the protein concentration was determined with BCA kit according to the manufacturer’s instructions. The peptides were obtained by digesting the protein with trypsin. Then, peptides were used for ubiquitin peptides enrichment by pre-washed antibody beads (PTM-1104, PTM Bio, Hangzhou, China). The subsequent quantitative ubiquitinome analysis was carried out by PTM Bio.