Abstract
Ovarian cancer diagnosis and the monitoring of ovarian cancer patients currently rely on the detection of the glycoprotein CA125 through a double-determinant immunoassay. This immunoassay may not provide accurate reporting of CA125 amounts in serum samples if the antibodies fail to detect all proteoforms (false negative results) or because of antibody binding to off-target proteins (false positive results). An immunoaffinity-free detection method, such as mass spectrometry-based bottom-up proteomics, would be an attractive alternative, but glycoproteins such as CA125 are notably challenging to analyze by such methods. Here, we demonstrate a proteomics workflow involving suspension trapping (STrap) sample preparation and deoxycholic acid as a passivating agent to reduce protein loss through adsorption; this approach enables improved protein coverage over conventional workflows (from 3 to 12% coverage of ascites-derived CA125). We expect that this rapid and simple sample preparation strategy will assist in the development of mass spectrometry-based assays for CA125 and other large glycoproteins. Graphical abstract.