Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Although standard-of-care chemotherapeutics are sufficient for most ALL cases, there are subsets of patients with poor response who relapse in disease. The biology underlying differences between subtypes and their response to therapy has only partially been explained by genetic and transcriptomic profiling. To characterize ALL subtypes and identify novel pharmacologic vulnerabilities, we performed comprehensive multi-omic analyses of 49 widely-used childhood ALL cell lines, using proteomics, transcriptomics, and pharmacoproteomic characterization. This enabled us to characterize the functional impact of genetic fusions and cellular differentiation states. The proteomics data revealed differences in spliceosome and p53 levels not evident in the transcriptomics data and with improved correlation to drug sensitivity. Focusing on BCP-ALL cell lines, we connected the genotype, molecular phenotype, and functional phenotype with drug response data on 528 oncology drugs. Here, we identified the DAG-analog Bryostatin-1 as a novel therapeutic candidate in the MEF2D-HNRNPUL1 fusion high-risk subtype, for which this drug activated pro-apoptotic ERK signaling associated with molecular mediators of pre-B cell negative selection. Our data also forms an interactive online resource with navigable proteomics, transcriptomics, and drug sensitivity profiles at https://lehtio-lab.se/forall/.