Native-state and cell type-specific proteomics using TurboID proximity labeling in mouse models

Proteome-level investigations of distinct cell types while retaining their native states in tissue can provide key insights into disease mechanisms that may not be captured by transcriptomic studies. We describe protocols to achieve cell type-specific in vivo biotinylation of proteins (CIBOP) in mouse brain. CIBOP uses a proximity labeling approach in which biotin ligase TurboID is expressed in specific cell types, leading to broad proteomic biotinylation. Subsequently, biotinylated proteins can be enriched from bulk tissue homogenates without requiring cell type isolation, followed by mass spectrometry-based quantitative proteomics of biotinylated proteins, yielding cell type-specific proteomes. We showcase CIBOP to label neurons and astrocytes, using adenovirus-based as well as transgenic approaches. This versatile pipeline may be readily applicable to various cell types as well as to neurological and non-neurological disease model systems.