Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells* Correspondence In Brief Graphical Abstract + Int. Ref Collection microreactor On-column TMT labeling bRP fractionation Long gradient, long column, high resolution LC-MS/MS

Abstract

A streamlined and readily accessible sample preparation protocol has been developed to enable TMT-based proteomic profiling of relatively low numbers of cells directly from a flow cytometer. These methods were applied to 12 freshly isolated immune cell types from mice to a depth of over 7000 quantified proteins. These data recapitulate many aspects of known immu-nology, nominate new cell type specific protein markers, and provide evidence for post-tran-scriptional regulation of gene expression across the immune system.