We developed a simplified proteomics sample preparation method that increased the sensitivity and reproducibility of large-scale plasma samples. Peptide loss was reduced while sensitivity was increased by eliminating the peptide clean-up step and using disposable trap column tips. The simplified High-Throughput Plasma Proteomics (sHTPP) method was evaluated using a systemic approach. We identified and quantified more than 500 proteins in non-depleted plasma samples without missing values as the DIA approach improved in terms of identification and quantification. Furthermore, 96-well plate sample handling with a multi-channel pipet allows for high-throughput sample analysis. In a large-scale clinical trial with 300 plasma samples, we used the method to demonstrate robust and accurate quantifications.