Abstract: Set forth herein are glycopeptide biomarkers useful for diagnosing diseases and conditions, such as ovarian cancer. Also set forth herein are methods of generating glycopeptide biomarkers and methods of analyzing glycopeptides using mass spectroscopy. Also set forth herein are methods of analyzing glycopeptides using machine learning systems.

Abstract: Provided herein are methods, devices, and kits for identifying glycosylated polypeptide biomarkers and signatures for progression of a disease or a condition, such as cancer, or and response of the disease or condition to a treatment, such as treatment with immune checkpoint blockade for cancer. Provided herein are methods of generating glycosylated polypeptide biomarkers and methods of analyzing glycosylated polypeptides using mass spectrometry. Provided herein are methods of validating a model using glycosylated polypeptides for predicting the disease or condition or for making treatment recommendation.