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Fig. 1 | Genome Biology

Fig. 1

From: SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

Fig. 1

Validating SCoPE-MS by classifying single cancer cells based on their proteomes. a Conceptual diagram and work flow of SCoPE-MS. Individually picked live cells are lysed by sonication, the proteins in the lysates are digested with trypsin, the resulting peptides labeled with TMT labels, combined and analyzed by LC-MS/MS (Orbitrap Elite). b Design of control experiments used to test the ability of SCoPE-MS to distinguish U-937 cells from Jurkat cells. Each set was prepared and quantified on a different day to evaluate day-to-day batch artifacts. c Unsupervised principal component (PC) analysis using data for quantified proteins from the experiments described in panel b stratifies the proteomes of single cancer cells by cell type. Protein levels from six bulk samples from Jurkat and U-937 cells are also projected and marked with filled semitransparent circles. The two largest PCs explain over 50% of the variance. Similar separation of Jurkat and U-937 cells is observed when different carrier cells are used (Additional file 1: Figure S2). d Distributions of protein levels across single U-937 and Jurkat cells indicate cell-type-specific protein abundances. e Adenocarcinoma cells (MDA-MB-231) expressing mCherry and LifeAct-iRFP670 were sorted by Aria FACS into a 96-well plate, one cell per well. The relative levels of mCherry and iRFP were estimated by the sorter (from their florescence intensity) and by SCoPE-MS, and the two estimates compared by their Spearman correlations (ρ)

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