High-throughput proteomics platform for clinical applications

Clinical proteomics holds the promise to accelerate the discovery of disease biomarkers, as well as to predict disease trajectories. Here we present a new platform for high-throughput plasma and serum proteomics, which combines an automated sample preparation workflow, robust high-flow liquid chromatography, and an optimized SWATH-MS acquisition scheme as well as data processing workflow. The process requires as little as 5uL serum or plasma and makes use of fast 5-minute chromatographic gradients. The dataset shows the robustness and precision of the workflow and consists of commercial plasma and serum samples that were distributed in 4 different 96 well plates and injected within a sample series of 417 serum injections. Further, the dataset includes of injections of a single sample (pooled from 32 prepared commercial serum samples) every 10 injections.