A SARS-CoV‑2 Peptide Spectral Library Enables Rapid, Sensitive Identification of Virus Peptides in Complex Biological Samples

On the basis of an analysis of (i)
SARS-CoV-2 virions, (ii) SARS-CoV-2-infected
VeroE6 cell lysates, and (iii) recombinant SARS-CoV-2 proteins expressed
in HEK 293 cells, here we present a comprehensive SARS-CoV-2 peptide
spectrum compendium, comprising 1682 high confidence peptide consensus
spectra derived from 1170 peptides (of various charge states) spanning
23 virus proteins. This high quality reference set can be used, e.g.,
for the selection of commonly observed virus peptides for use in targeted
proteomics or data-independent acquisition (DIA) approaches. Using
this rich resource, we also demonstrate that a spectral matching search
approach yields improved performance over the use of standard database
search engines alone for the identification of virus peptides in complex
biological samples.