Understanding how proteins interact with each other to exert biological function has been essential for elucidating the causes and developing treatments for cancer. Cancer researchers continue to devote prodigious effort towards developing and refining methods for detecting and quantifying protein-protein interactions (PPI). Although numerous methods are available to study PPIs most technologies suffer from high false positive rates, missed biophysical interactions, strong biases towards abundantly expressed genes or detecting protein complexes, low throughput and lack of quantification. Moreover, most methods are not compatible for testing clinical material such as immune responses in patient serum. Therefore, there is a great need for multiplexed, robust technologies for quantitative profiling of protein interactions and early detection of immune responses. We have developed an innovative next-generation, in-solution protein microarray platform MISPA which exploits the extraordinary potential of next generation DNA sequencing (NGS) to address unanswered questions in cancer biology such as identifying unknown protein interactions, and early screening. MISPA is a solution phase functional protein microarray platform where each protein is uniquely barcoded with DNA. The barcoded protein cocktail is then interacted in solution with a query protein or clinical sample. We tested the feasibility of MISPA as a robust, multiplexed diagnostic tool for early screening of HPV positive oropharyngeal carcinomas (OPC). The proteomes of 12 different serotypes of HPV (96 antigens) was barcoded and tested against HPV positive OPC serum and control samples. MISPA showed distinct enrichment of certain HPV antibodies (HPV16E1, HPV16E2, HPV16E6 and HPV16E7) in the OPC patient samples compared to controls. We also noticed enriched immune response against other virulent HPV strains. The assay showed high reproducibility with an average %CV of 3.4. It also demonstrated an expanded dynamic range (> 104) with a 30-600 fold signal over background.