In our previous study, we found VPS28 (vacuolar protein sorting 28 homolog) could alter ubiquitylation level to regulate milk fat synthesis in BMECs (bovine primary mammary epithelial cells). While the information on the regulation of VPS28 on proteome of milk fat synthesis is less, we explored its effect on milk fat synthesis using iTRAQ (isobaric tags for relative and absolute quantitation) assay after knocking down VPS28 in BMECs. We found 2,773 proteins in three biological replicates with less than in 1.2% false discovery rate were identified and quantified. Among them, a subset of 203 proteins were screened as significantly down-(111) and up-(92) regulated inVPS28 knockdown BMECs compared with the control groups. According to Gene Ontology analysis, the differentially expressed proteins were enriched in the "proteasome", "ubiquitylation", "metabolism of fatty acids", "phosphorylation", and "ribosome". Meanwhile, some changes occurred in the morphology of BMECs and an accumulation of TG (triglyceride) and dysfunction of proteasome were identified, and a series of genes associated with milk fat synthesis, ubiquitylation and proteasome pathways were analyzed by RT-QPCR (quantitative real-time PCR). The results of this study suggested VPS28 regulated milk fat synthesis was mediated by ubiquitylation, it could be an important new area of study for milk fat synthesis and other milk fat content traits in bovine.