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

Abstract

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.