How to perform quantitative single cell proteomics with SCoPE2

The fate and physiology of individual cells are controlled by protein interactions. We recently developed SCoPE-MS, a method for direct analysis of proteomes of single cells by LC-MS/MS. SCoPE-MS is enabled by isobaric-tag multiplexing of peptides from single cells together with carrier material, which serves both to minimize sample losses to equipment surfaces and enhance peptide identifications. Yet, our ability to quantitatively analyze proteins in single cells has remained limited. To overcome this barrier, we developed SCoPE2. SCoPE2 lowers cost and hands-on time by introducing automated and miniaturized sample preparation while increasing quantitative accuracy using only commercially available equipment and reagents. Additionally, SCoPE2 accomplishes increased sample preparation throughput and increased measurement throughput. Using SCoPE2, we quantified over 2,700 proteins in 1,018 single monocytes and macrophages in 10 days of instrument time, and the quantified proteins allowed us to discern single cells by cell type. Parallel measurements of transcripts by 10x Genomics scRNA-seq indicate that most genes had similar responses at the protein and RNA levels, though the responses of hundreds of genes differed. In this talk, we present users with how to begin adopting SCoPE2 in their lab. Executing a SCoPE2 experiment has similarities to conventional proteomics sample preparation as well as pitfalls and deviations unique to working with single cells. We discuss successful strategies, including study design and reagent selection, how to avoid common pitfalls, and the range of common equipment that can be used to execute SCoPE2 sample prep. Additionally, we discuss approaches to optimizing LC-MS/MS instrumentation for SCoPE2 samples. We hope to give users ideas about how to successfully design and execute a SCoPE2 experiment to facilitate the broad adoption of automated and quantitative single-cell analysis of proteins by mass-spectrome.