Comparison of two multiplexed technologies for profiling >1,000 serum proteins that may associate with tumor burden – a pilot study

Background: In this pilot study, we perform a preliminary comparison of two targeted multiplex proteomics technologies for discerning serum protein concentration changes that may correlate to tumor burden in ovarian cancer (OC) patients. Methods: Using the proximity extension assay (PEA) and Quantibody® Kiloplex Array (QKA), we measured >1,000 proteins in pre-surgical and post-surgical serum from nine OC patients (N=18 samples). We expect that proteins which decreased significantly in concentration post-surgery may correlate to tumor burden in each patient. Duplicate sera from two healthy individuals were used as controls (N=4 samples). We employed in-house ELISAs to measure five proteins with large serum concentration changes in pre- and post-surgical sera from four of the original nine patients and the two original controls. Results: Both platforms showed weak correlation with clinical CA125 data. The two multiplexed platforms showed significant correlation with each other for >400 overlapping proteins. PEA uncovered 15 proteins, while QKA revealed 11 proteins, with more than a two-fold post-surgical decrease in at least six of the nine patients. Validation using single ELISAs showed at least a two-fold post-surgical decrease in serum concentration in the same patients as observed by the two multiplex assays. Conclusion: Both methods identified proteins that considerably decreased in concentration post-surgery in OC patients and have already been implicated in OC. Our findings from a limited sample size suggest that novel targeted proteomics platforms are promising tools for identifying candidate serological tumor-related proteins, but independent technical validation is essential to improve accuracy and avoid false discoveries.