Herein, we have utilized two cellular models of epithelial ovarian cancer (EOC), where transfer of normal chromosome 18 material into the EOC cell lines TOV-112D and TOV-21G induced in vitro and in vivo suppression of tumorigenic phenotype in derived hybrid clones. Two-dimensional-liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) with tandem mass tagging (TMT) was then employed to profile the whole cell, secreted and crude membrane proteomes of the parental and hybrid cell models to identify differentially expressed proteins as potential markers of ovarian tumor suppression. Protein changes of interest were confirmed by immunoblotting in additional hybrid and revertant cell lines. This method afforded quantitative coverage of around 1,000 unique proteins and is applicable to the analysis of any cell model, tissue or biofluid.