Enhanced Lipidomics Analysis of Breast Cancer Cells Using Three‐phase Liquid Extraction and Ultra High‐performance Liquid Chromatography Coupled With Quadrupole Time‐of‐Flight Tandem Mass Spectrometry

ABSTRACT Lipid extraction of complex biological samples is essential for high‐quality data in liquid chromatography‐mass spectrometry (LC‐MS)‐based lipidomics. This study introduces a three‐phase liquid extraction (3PLE)‐ultra‐high‐performance LC coupled with quadrupole time‐of‐flight tandem MS method. This method was successfully applied to lipidomics analysis of breast cancer cells, including highly metastatic MDA‐MB‐231 and slightly metastatic MCF7 cells. The 3PLE method employed an n ‐hexane/methyl tert‐butyl ether/acetonitrile/water solvent system that formed one aqueous and two organic phases. Neutral and polar lipids were enriched in the upper and middle organic phases, respectively, and combined for detection, thereby reducing analysis time. Compared with the Bligh and Dyer method, 3PLE achieved higher sensitivity and detected more features, with over a 50% increase in the relative abundance of nearly 50% of the differential lipids. In total, 21 differential lipids were identified in the MDA‐MB‐231 group and 22 in the MCF7 group compared to normal breast epithelial cells (MCF10A). Pathway analysis suggested that lipid changes in breast cancer cells were associated with glycerophospholipid metabolism, arachidonic acid metabolism, sphingolipid metabolism, and linoleic acid metabolism. The study presents a highly efficient lipidomics method, providing a scientific foundation for understanding breast cancer pathogenesis and aiding in diagnosis.