Slavov lab | Quantitative Biology
Supporting  Information
Automated sample preparation for high-throughput single-cell proteomics

Summary

A major limitation to applying quantitative mass spectrometry-based proteomics to small samples, such as single cells, are the losses during sample cleanup. To relieve this limitation, we developed a Minimal ProteOmic sample Preparation (mPOP) method for culture-grown mammalian cells. mPOP obviates cleanup, and thus eliminates cleanup-related losses while simplifying and expediting sample preparation. Bulk SILAC samples processed by mPOP or by conventional urea-based methods indicated that mPOP results in complete cell lysis and accurate relative quantification. Combining mPOP with cell-sorting and liquid handling of U-937, HEK293 and Jurkat cells, we can prepare hundreds of Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) samples per day and can process 12 such samples, equivalent to 96 single cells, per day per instrument. Using this approach, we quantify thousands of proteins across 96 single cells. Likewise, mPOP enables protein measurements in 10, 20, and 100 cell samples with unprecedented breadth and throughput.