Data-Independent Acquisition Analysis to Identify Serum Biomarkers and Neoantigens for Differentiating Colorectal Cancer from Inflammatory Bowel Diseases

Early colorectal cancer (CRC) detection among inflammatory bowel disease improves treatment outcomes and survival. A sensitive and specific serum-based tool can bridge the gap between patient presentation and invasive colonoscopy, thereby enhancing early diagnosis. We screened serum biomarkers in colonoscopy-positive (CP, cancer) and colonoscopy-negative (CN, other bowel diseases) individuals, as well as in healthy controls (<i>n</i> = 20 each), to identify CRC-specific markers. Using data-independent acquisition-mass spectrometry, three proteins were identified as uniquely altered in the CP group compared with CN. We found that a serum protein called brain-specific angiogenesis inhibitor I-associated protein 3 was significantly overexpressed in CRC patients, which can distinguish CP patients from CN patients. Additionally, 19 neoantigen peptides specific to the CRC serum proteome were identified. Further validation in an independent set of samples (<i>n</i> = 10 per group) using parallel reaction monitoring was performed for the potential biomarker and neoantigen identified. These proteins were combined with carcinoembryonic antigen into a multiprotein panel, which enhanced diagnostic performance (AUC = 0.758), yielding 67% sensitivity, 64% specificity, and 65% accuracy. These findings support the potential of a targeted serum-based panel for preselecting symptomatic individuals for colonoscopic evaluation. However, further studies are needed in a larger cohort to evaluate clinical utility.