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


A major limitation to applying quantitative LC-MS/MS proteomics to small samples, such as single cells, are the losses incured 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 expediting sample preparation and simplifying its automation. Bulk SILAC samples processed by mPOP or by conventional urea-based methods indicated that mPOP results in complete cell lysis and accurate relative quantification. We integrated mPOP lysis with the Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) sample preparation, and benchmarked the quantification of such samples on a Q-exactive instrument. The results demonstrate low noise and high technical reproducibility. Then, we FACS sorted single U-937, HEK-293, and mouse ES cells into 96-well plates and analyzed them by automated mPOP and SCoPE-MS. The quantified proteins enabled separating the single cells by cell-type and cell-division-cycle phase.

Minimal ProteOmic sample Preparation (mPOP)

quantifying proteins in Single cells

Single-Cell ProtEomics by Mass-Spectrometry (SCoPE-MS)

Single cell proteomics by Mass-spec (SCoPE-MS)

Explore the Mass-spec data

Specht H, Harmange G, Perlman DH, Emmott E, Niziolek Z, Budnik B, Slavov N. (2018)
Automated sample preparation for high-throughput single-cell proteomics
bioRxiv   DOI: 10.1101/399774   PDF   |   RAW Data @ MassIVE   |   RAW Data @ ProteomeXchange   |   SCP2018 Talk