To test the performance of our method, we measured the abundances of 25 protein phosphorylation sites, three housekeeping proteins, and three phenotypical markers in conjunction with the cell-volume and cell-cycle markers (Supplementary Table 1) in HEK293T (embryonic kidney), MDA-MB-231 (breast cancer), and THP-1 (monocyte) cells that had been stimulated with TNFα for 0, 5, 10, 15, 30, and 60 min (Methods). The gene discussed is TNF; the disease is breast carcinoma.