The project aims to examine the protein level changes under induced mitochondrial abasic site lesions in HeLa cells using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics. The data revealed significant changes in the expression level of several proteins. A decrease in mitochondrial ribosomal proteins (MRPS35, MRPL15, MRPL37, MRPL13, and MRPL4) and complex I subunits (NDUFA12 and NDUFA13) was observed, suggesting a suppression of mitochondrial protein synthesis and energy production under these conditions. In addition, the levels of ARF5 (ADP ribosylation factor 5), DNM1L (dynamin-1-like protein), and PRDX6 (peroxiredoxin 6) were upregulated. ARF5 is involved in protein trafficking, and DNM1L mediates mitochondrial and peroxisomal division.