a Comparison of the PCA and UMAP embeddings resulting from the imputed protein matrix. Number of proteins refers to the non-imputed proteins measured per cell. ‘Medium’=302 cells, ‘high’=255 cells. BLAST = blasts, LSC = leukemia stem cells, PROG = progenitors. b Separation of populations measured by the silhouette coefficients of progenitors and LSCs calculated in UMAP space for 300 ms (n = 219) and 500 ms (n = 166). Boxplot shows median, 0.25 and 0.75 quantile, and whiskers extend to points within 1.5 interquartile range of lower and upper quartile. c Pearson correlation of the protein fold changes (log2FC) between blasts and LSCs measured in the scMS workflow and MS3 bulk-sorted data. Non-imputed values were used and only proteins with ≥3 values in blasts and LSCs respectively were considered. Number of proteins in 300 ms and 500 ms is n = 1725 and n = 1342, respectively. d Same analysis as in panel c, but with the top 400 high-coverage proteins selected for each dataset. e Absolute log2FC difference of proteins of LSC vs. blast between scMS and MS3 bulk-sorted data across intensity bins. Only proteins that were significantly changed between LSC and blast in the MS3 bulk-sorted data were selected for comparison (FDR < 0.05, absolute log2FC > 0.5). Proteins were binned across their mean log2 signal-to-noise (S/N) in the 300 ms and 500 ms dataset. n= number of proteins with absolute fold change difference plotted. Boxplot shows median, 0.25 and 0.75 quantile, and whiskers extend to points within 1.5 interquartile range of lower and upper quartile. Outliers not shown. f log2FC of selected proteins in 300 ms, 500 ms, and MS3 bulk-sorted data. Proteins were binned into 12 bins across their mean log2 S/N in the 300 ms and 500 ms dataset. From each bin the protein with the highest absolute fold-change between LSC and blast in the MS3 bulk-sorted data was selected for comparison with scMS ratios. Source data are provided as a Source Data file.