Large-cohort proteomics analysis using mass spectrometry is a powerful approach to discover and validate new biomarkers. In combination with clinical data and computational analysis, large-cohort proteomics study brings opportunities in improving early diagnosis, refining patient stratification, and predicting/monitoring treatment response. Yet, to achieve meaningful biological insights in large-cohort studies, robust, reproducible, and comprehensive proteome profiling in a high-throughput manner still remains challenging.
Here, we use a novel high-resolution accurate mass (HRAM) platform to enable high-quality and robust protein quantification across thousands of LC-MS/MS analyses. With a throughput of 100 samples/day, we can reproducibly profile ~9000 proteins from human cell line and ~700 proteins from undepleted plasma across multiple instruments and more than 10 consecutive days in a 24/7 operation mode.