To investigate the effect of ATP2 knockdown on the protein expression of Candida albicans, we performed proteomic assays for atp2Δ/Δ and wild type strains. A total of 4000.0 proteins were identified in this study, of which 3652.0 proteins contained quantitative information. If a 1.5-fold differential expression change threshold and a statistical test t-test p-value < 0.05 were used as the significance threshold, then among the quantified proteins, we found that 112 proteins were up-regulated and 268 proteins were down-regulated in atp2Δ/Δ cells. Based on the above data, we performed systematic bioinformatics analysis (protein functional annotation) of all identified proteins, and performed functional classification, functional enrichment and functional enrichment-based clustering analysis of all differentially expressed proteins.