Flow cytometry has a significant impact on the cellular metabolome (CE-MS assay)

The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyse the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signalling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry. The CE-MS assay is reported in the current study MTBLS633. The General LC-MS assay is reported in MTBLS629. The Lipidomic LC-MS assay is reported in MTBLS631. The GC-MS assay is reported in MTBLS634. Linked Studies: MTBLS629 MTBLS631 MTBLS634