FGT-METAP (Female Genital Tract Metaproteomics) is an application for exploring and mining the FGT microbial composition and function of young and adolescent HIV-uninfected South African women (n=113) at high risk of HIV infection. FGT metaproteomic data was generated using shotgun liquid chromatography-tandem mass spectrometry. Women were grouped as having low, medium or high FGT pro-inflammatory cytokine or chemokine concentrations using K-means clustering. FGT samples were screened for common sexually transmitted infections (STIs), including Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, Mycoplasma genitalium, and herpes simplex virus type 2. Bacterial vaginosis (BV) was assessed by Nugent scoring. Prostate-specific antigen (PSA) was measured in FGT samples as a marker of recent semen exposure.