Mitoxantrone (MX) is regularly used to treat several cancers, yet despite its long history in the clinic, recent studies continue to unveil novel protein targets that may contribute to the cytotoxic effects of the drug, as well as potential non-canonical antitumor activity. A better understanding of MX’s cellular targets is required to fully comprehend the molecular consequences of treatment and to interpret MX-sensitivity in homologous recombination (HR)-deficient cancer. The mass spectrometry samples reported here represent the analysis of MX impacts on proteoform abundance in HR-deficient or proficient UWB1.289 ovarian cancer cells using TMT-labeled quantitative proteomics.