High-Throughput Single-Cell Lipid Mass Cytometry for Rapid and Robust Screening of Rare Cells

Single-cell lipid mass cytometry holds immense potential for functional phenotyping but is hindered by low throughput. To address this, we developed a high-throughput platform integrating a flow-focusing ionization source with a high-resolution time-of-flight mass spectrometer. This system achieved a maximum throughput of 1064.5 cells/min, representing a 20-fold increase over existing methods such as CyESI-MS (∼38 cells/min) and ILCEI-MS (∼51 cells/min). It enabled the detection and identification of 141 lipids from single cells for precise metabolic phenotyping. When applied to a peripheral blood mononuclear cell assay, the platform successfully analyzed and subtyped complex immune cell populations. Notably, it achieved the rapid, label-free identification of rare dendritic cells with an abundance as low as 1.53% within 3 min. This platform enables efficient screening of rare immune cell subsets based solely on metabolic signatures, establishing a robust foundation for immunology and translational medicine.