In this study, H1975 wild-type and MPND-knockout cells were used for SILAC-based quantitative ubiquitin proteomics. Ubiquitinated peptides were enriched and analyzed by nano-LC-MS/MS. MaxQuant was used for protein quantification and differential ubiquitination site screening. Bioinformatic analyses including GO, KEGG and PPI network analysis were performed to explore the molecular mechanism and downstream substrates regulated by MPND.