a Diffusion map based on imputed scMS data (2,025 cells, 2,723 proteins) overlaid with FACS derived cell gating and CD34 and CD38 expression. BLAST = blasts, PROG = progenitors, LSC = leukemia stem cells. b Left: Diffusion map overlaid with pseudotime, calculated using the scMS data. Middle: Scatterplot of cells with their calculated pseudotime and FACS derived CD38 expression, annotated with their gating (middle) or CD34 expression (left). c Heatmap of cells in the columns ordered in pseudotime and 479 selected proteins (Methods) in the rows. Proteins were clustered hierarchically into five clusters. Imputed protein expression values, CD34, CD38 and pseudotime for the ordered cells were smoothed by applying a moving average across 50 cells. Protein expression is normalized between 0 and 1. d Expression values of all proteins in each cluster were aggregated to a signature by taking the mean and normalizing between 0 and 1. Top: Signatures are plotted on top of the diffusion map. Bottom: Scatterplot of cells with their pseudotime and the signature of each cluster, annotated with their gating. Source data are provided as a Source Data file.