Cell-Type-Specific Surfaceome Profiling of 100-500 Isolated Cells using a Droplet-Based Magnetic Affinity Purification System
Lorentzian, A. C.; Bartleson, J. M.; Ho, T.; Yang, Z.; Choi, M.; Cheung, T. K.; Rose, C. M.; Yewdell, W. T.; Zhu, Y.
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Cell surface proteins (CSPs) represent an important source of biomarkers and therapeutic targets. However, due to the inherent sensitivity limitations of existing technologies, tissue and cell-type-specific surfaceomes remain poorly characterized, especially in the context of human diseases. Herein, we develop nanoMAPS (nanoscale Magnetic Affinity Purification System), a miniaturized proteomic sample preparation method for surfaceome profiling of as few as 100-500 cells (1000x to 100,000x lower than existing technologies). We demonstrate that the miniaturization of magnetic bead-based affinity purification inside a single droplet can efficiently improve the recovery of surface proteins and reduce non-specific absorption of intracellular proteins. By applying nanoMAPS to human immune cells isolated from PBMCs, we demonstrate robust identification of both well-known cell-type-specific surface markers and candidate proteins. We establish nanoMAPS as a promising platform to expand surface proteomics from cultured cells to primary cells isolated from patients or mouse models.
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