Simple and robust high-throughput serum proteomics workflow with low-microflow LC-MS/MS

Abstract

Clinical proteomics has substantially advanced in identifying and quantifying proteins from biofluids, such as blood, contributing to the discovery of biomarkers. The throughput and reproducibility of serum proteomics for large-scale clinical sample analyses require improvements. High-throughput analysis typically relies on automated equipment, which can be costly and has limited accessibility. In this study, we present a rapid, high-throughput workflow low-microflow LC？MS/MS method without automation. This workflow was optimized to minimize the preparation time and costs by omitting the depletion and desalting steps. The developed method was applied to data-independent acquisition (DIA) analysis of 235 samples, and it consistently yielded approximately 6000 peptides and 600 protein groups, including 33 FDA-approved biomarkers. Our results demonstrate that an 18-min DIA high-throughput workflow, assessed through intermittently collected quality control samples, ensures reproducibility and stability even with 2 ？L of serum. It was successfully used to analyze serum samples from patients with diabetes having chronic kidney disease (CKD), and could identify five dysregulated proteins across various CKD stages.