Cell-type-specific surfaceome profiling of 100-500 isolated cells using a droplet-based Magnetic Affinity Purification System

Cell surface proteins 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. Here, we present nanoMAPS (nanoscale Magnetic Affinity Purification System), a miniaturized proteomic sample preparation method for surfaceome profiling of as few as 100-500 cells (~100,000-fold lower than existing technologies). By performing magnetic bead-based affinity purification within a single microliter-scale droplet, nanoMAPS significantly improves the recovery of surface proteins and reduces non-specific absorption of intracellular proteins. Application of nanoMAPS to primary human immune cells and mouse plasma cell populations enables robust identification of established cell-type-specific surface markers as well as other proteins selectively enriched in disease-associated immune cell subpopulations. Together, these results establish nanoMAPS as a broadly applicable platform for extending surface proteomics technology to rare primary cells isolated directly from diseased tissues. Surface proteins are a key source of biomarkers and therapeutic targets, but remain poorly characterized in disease-relevant cells. Here, authors developed nanoMAPS, an ultrasensitive proteomic method to profile surface proteins from hundreds of primary cells and identify potential biomarkers.