Fig. 4

Guidelines for the manual validation of MS/MS spectra using the Multi-omic Visualization Platform (MVP). The MS/MS spectra of peptides that passed validation in PepQuery were manually annotated using MVP based on a test cohort of four peptides that passed validation in COVID-positive patient datasets and two peptides that passed validation in COVID-negative patient data. The signal-to-noise ratio of the product ions within MS/MS spectra was examined, and spectra containing product ions with at least a three-fold higher intensity than noise level were retained. Next, the degree of completeness of the b- and y-ion series was considered, with passing spectra determined to have at least three consecutive b- or y-ions in their series. Peptides with spectra that passed these criteria were considered valid peptide targets for the detection of SARS-CoV-2