In this study, we isolated CD133-positive and counterpart CD133-negative subsets from human liver cancer cell line PLC8024 followed by metabolomics study based on Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS) and ultrahigh-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS) to profile the cellular metabolome. This evidence concerns the gene PROM1 and liver cancer.