Our biological understanding of and treatment options for the deadliest gynecological malignancy epithelial ovarian cancer (EOC) are still inadequate because of EOC heterogeneity and unresolved controversy regarding its tissue-of-origin. Here, we define the molecular landscape of EOC and compare it to healthy ovarian tissues, ovarian surface epithelium (OSE) and the distal fallopian tube epithelium (FTE), by analyzing minute amounts of patient-derived cells by single-shot mass spectrometry-based phosphoproteomics. We provide a resource of differentially expressed proteins and phosphorylation sites that discriminate EOC from healthy tissues. A multi-disciplinary validation of these results proved that patient-derived epithelial cells recapitulate well EOC complexity. The quantitative phosphoproteomics dataset revealed that the cyclin-dependent kinase 7 (CDK7), although active in both FTE and EOC, was associated with RNA polymerase II (POLR2A) activation only in patient-derived cancer samples and cancer cell lines. Finally, we demonstrate that CDK7 controls EOC cell proliferation and that blocking CDK7 activity by a small molecule inhibitor specifically killed ovarian cancer cells. Our work provides a global portrait of EOC biology, paving the way for efficient prognostic and therapeutic approaches for EOC patients.