Fig. 3

Principal component analysis of differentiating ES cells. a Distributions of protein abundances for all proteins quantified from 10⁷ differentiating ES cells [17] or in at least one single-cell SCoPE-MS set at FDR 1%. The probability of quantifying a protein by SCoPE-MS is close to 100% for the most abundant proteins quantified in bulk samples and decreases with protein abundance, for a total of 1526 quantified proteins. b The proteomes of all single EB cells were projected onto their PCs, and the marker of each cell color-coded by day. The single-cell proteomes cluster partially based on the days of differentiation. c A tabular display of the variance explained by the principal components from panel c and their correlations to the days of differentiation and the missing data points for each cell. d, e The proteomes of cells differentiating for 8 days were projected onto their PCs, and the marker of each cell color-coded based on the normalized levels of all proteins from the indicated gene-ontology groups