Fig. 5: Analysis of single TE and hPS cells.
Individual cells were isolated using FACS into a 384-well plate. Digested cells were analyzed at 50 SPD using the optimized settings for LC and MS on the Orbitrap Astral mass spectrometer. a, Circles indicate identified PGs at a 1% FDR of each individual cell, bars indicate the mean values, and error bars indicate standard deviations. The dataset contains 21 and 12 individual hPS cells and TE-like cells, respectively. The search was performed library free in method evaluation mode or DirectDIA+ or against a tailored library created from three replicates of 100 cells each prepared in the exact same way but recorded with adopted settings (that is, 60 ms IT and m/z 20 windows for single cells, 10 ms IT and m/z 5 windows for 100 cells). Blanks (n = 4) were processed in the same 384-well plate and contained all reagents and buffers but no cells. b,c, The PCA (b) and UMAP (c) are based on protein quantities, with each dot representing a cell and colors reflecting the cell type based on fluorescent marker proteins.
