To elucidate potential markers of endometriosis and Background: endometriosis-associated endometrioid and clear cell ovarian carcinomas using mass spectrometry-based proteomics. A total of 21 fresh, frozen tissues from patients diagnosed with clear Methods: cell carcinoma, endometrioid carcinoma, endometriosis and benign endometrium were subjected to an in-depth liquid chromatography-tandem mass spectrometry analysis on the Q-Exactive Plus. Protein identification and quantification were

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... d using MaxQuant, while downstream analyses were performed using Perseus and various bioinformatics databases. Approximately 9000 proteins were identified in total, representing the Results: first in-depth proteomic investigation of endometriosis and its associated cancers. This proteomic data was shown to be biologically sound, with minimal variation within patient cohorts and recapitulation of known markers. While moderate concordance with genomic data was observed, it was shown that such data are limited in their abilities to represent tumours on the protein level and to distinguish tumours from their benign precursors. The proteomic data suggests that distinct markers may Conclusions: differentiate endometrioid and clear cell carcinoma from endometriosis. These markers may be indicators of pathobiology but will need to be further investigated. Ultimately, this dataset may serve as a basis to unravel the underlying biology of the endometrioid and clear cell cancers with respect to their endometriotic origins.