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

Jonathan R St-Germain; Audrey Astori; Brian Raught

doi:10.1021/acs.jproteome.1c00048

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

J Proteome Res. 2021 May 7;20(5):2187-2194. doi: 10.1021/acs.jproteome.1c00048. Epub 2021 Mar 8.

Authors

Jonathan R St-Germain¹, Audrey Astori¹, Brian Raught^{1

2}

Affiliations

¹ Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2C4, Canada.
² Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

PMID: 33683136
DOI: 10.1021/acs.jproteome.1c00048

Abstract

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.

Keywords: COVID-19; SARS-CoV-2; SpectraST; coronavirus; mass spectrometry; proteomics; spectral library; spectral matching.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
HEK293 Cells
Humans
Peptide Library*
Peptides
SARS-CoV-2
Tandem Mass Spectrometry

Substances

Peptide Library
Peptides