EGFR and squamous cell carcinoma: To demonstrate VESPA’s applicability to this dataset, we applied the algorithm to the phosphoproteomic profiles for A431 epidermoid carcinoma cells (dependent on EGFR expression), perturbed by afatinib (targeting EGFR), gefitinib (targeting EGFR), and dasatinib (targeting SRC- and EPH-family proteins) with 10 different drug concentrations (Supplementary Fig. 5, Methods).