Aberrant glycosylation and changes in cell surface carbohydrate structures in tumors is known to occur in many cancer processes. Widely used clinical diagnostic tests for cancer target glycoproteins or glycan epitopes including carcinoembryonic antigen, CA-125, prostate-specific antigen, and CA-19-9. We recently developed an efficient and robust lectin-affinity chromatography and MS-based workflow to enrich for glycopeptides bearing cancer-related carbohydrates. Since then, our interlaboratory initiative carried out a two-phase glycopeptide-based study to first discover breast cancer relevant glycoproteins by analyzing conditioned medium from breast cancer cell lines, and secondly, to use those results to direct the design of peptide-specific multiple reaction monitoring (MRM) assays that can be used to analyze their levels in the plasma of breast cancer and control patients.
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