Updated project metadata. Cervical mucus is a viscous fluid functioning as a uterine cervix plug. It is formed and produced by cervical glands located in the cervix. During ovulation, cervical mucus starts to become less viscous, which is a good window for non-invasive sampling. Our study focuses on the proteomic characterization of cervical mucus, which may thus act as a non-invasively acquired source of biomarkers for diseases and physiological conditions of the female genital tract. Our study aimed at two aims - the first is to optimize a proteomic workflow of cervical mucus processing. The second aim is to assess differences in the proteomic composition of cervical mucus in natural ovulatory cycles and IVF cycles with controlled ovarian hyperstimulation. The sampling was done in cooperation with women undergoing intrauterine insemination in a natural ovulatory cycle and women undergoing controlled ovarian hyperstimulation for IVF. The optimization of proteomic workflow including an analysis on an Orbitrap mass spectrometer was performed. The results revealed the protein composition and the differences of the cervical mucus between natural and stimulated uterus.