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. 2020 Jul;20(14):e2000107.
doi: 10.1002/pmic.202000107. Epub 2020 Jun 21.

Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data

Duarte Gouveia  1 , Lucia Grenga  1 , Jean-Charles Gaillard  1 , Fabrice Gallais  1 , Laurent Bellanger  1 , Olivier Pible  1 , Jean Armengaud  1
Affiliations

Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data

Duarte Gouveia et al. Proteomics. 2020 Jul.

Abstract

Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial tool for fighting the COVID-19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS-CoV-2 infected Vero cells. Proteins from inactivated virus samples were extracted, digested with trypsin, and the resulting peptides were identified by data-dependent acquisition tandem mass spectrometry. The 101 peptides reporting for six viral proteins were specifically analyzed in terms of their analytical characteristics, species specificity and conservation, and their proneness to structural modifications. Based on these results, a shortlist of 14 peptides from the N, S, and M main structural proteins that could be used for targeted mass-spectrometry method development and diagnostic of the new SARS-CoV-2 is proposed and the best candidates are commented.

Keywords: COVID-19; SARS-CoV-2; mass spectrometry; peptides; proteomics; viral protein detection.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Retention times and peak areas from the 16 precursor ions identified from the skyline analysis.
Figure 2
Figure 2
Sequence variants identified for each of the 14 peptides from Table 1. The sequences of these peptides are indicated in bold. Variants were identified through multiple sequence alignments of the ten viral proteins from virus Italy‐INMI1 strain with other sequenced human SARS‐CoV‐2, bat, and pangolin closely related viruses. Variations in the amino acid sequences are highlighted in red.
See this image and copyright information in PMC

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