SARS-CoV-2_PRM_SRM_targeted_acquisitions

The current outbreak of severe acute respiratory syndrome associated with coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. We developed a high-throughput targeted proteomics assay to detect SARS-CoV-2 proteins directly from nasopharyngeal and oropharyngeal swabs. Sample preparation was fully automated by using a modified magnetic particle-based proteomics approach implemented on a robotic liquid handler. The use of turbulent flow chromatography included four times multiplexed on-line sample cleanup and liquid chromatography separation. Mass spectrometry detection of nucleoprotein peptides was achieved within 2.5 min, enabling the analysis of more than 500 samples per day. The method was validated qualitatively (Tier 3) and quantitatively (Tier 1) using 855 specimens previously analyzed by real-time RT-PCR and was able to detect up to 84% of positive cases with up to 97% of specificity. The strategy here presented has high sample stability and should be considered as an option for testing in large populations.