Development and Clinical Evaluation of a Multiplexed Health Surveillance Panel Using Ultra High-Throughput PRM-MS in an Inflammatory Bowel Disease Cohort

Despite advances in clinical proteomics, translating protein biomarker discoveries into clinical use remains challenging due to the technical complexity of the validation process. Targeted MS-based proteomics approaches like Parallel Reaction Monitoring offer sensitive and specific assays for biomarker translation. In this study, we developed a multiplex PRM assay using the combination of the Stellar-MS platform and the ART algorithm to quantify 57 plasma proteins, including 21 FDA-approved proteins. Loading curves (11-points) were conducted at 4 sample throughputs (100, 144, 180, and 300 samples per day) using independent, optimized, and scheduled PRM methods. Following optimization, an inflammatory bowel disease (IBD) cohort of plasma sample (496 IBD, 511 matched controls) was analyzed at a throughput of 180 SPD. To monitor system performance, the study also included 2,000 additional injections for system suitability tests, low, mid, and high-quality controls, washes, and blanks. Using this approach, we observed high quantifiability (linearity, sensitivity, reproducibility) in the PRM assay and consistency in data acquisition across a large cohort and validated the candidate IBD markers observed from discovery, particularly, CRP and A1AG1.