Small molecule metabolite extraction strategy for improving LC/MS detection of cancer cell metabolome

Metabolomics is the comprehensive assessment of endogenous metabolites of a biological system. "Oncometabolomics" is a rapidly emerging field with potential for developing specific biomarkers for early detection, diagnosis, and disease prognosis. Given the power of this technology, the availability of standardized sample preparation methods for immortalized human cancer cell lines is critical toward augmenting research in this direction. Using MCF-7 cells as a model system, we describe an approach for intracellular metabolite extraction from cell cultures for reproducible and comprehensive metabolite extraction. The samples, when injected onto a reverse-phase 50 × 2.1 mm Acquity 1.7-μm C18 column, using an ultra performance liquid chromatography system (UPLC) coupled with electrospray ionization-quadrupole-time-of-flight-mass spectrometry (ESI-Q-TOF-MS) in positive and negative modes, yielded a data matrix with a total of 2600 features. This method, when compared with a water-extraction procedure described earlier, was found to yield significantly higher coverage and detection of molecular features. Finally, we successfully tested the performance of this method for an array of human cancer cell lines used widely in the cancer research field.