The response to anticancer therapies is limited by drug resistance, part of which can be explained by tumor genomics (Vasan et al. Nature 2019). In contrast, we have little understanding of how anticancer therapies modulate the tumor proteomes of patients. Recent advances in mass spectrometry now permit unbiased proteomics of formalin-fixed paraffin-embedded (FFPE) tissue, which is how the majority of archival tumor specimens are stored. We are performing proteomic profiling of cohorts of FFPE breast tumors from patients exposed to chemotherapies and targeted therapies, in collaboration with our clinical colleagues, in order to nominate and test new proteomic markers of therapeutic resistance and response.