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Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

Karel Bezstarosti, View ORCID ProfileMart M. Lamers, Wouter A.S. Doff, Peter Wever, Khoa Thai, Jeroen J. A. van Kampen, View ORCID ProfileBart L. Haagmans, View ORCID ProfileJeroen A. A. Demmers
doi: https://doi.org/10.1101/2020.04.23.057810
Karel Bezstarosti
1Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
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Mart M. Lamers
2Viroscience Department, Erasmus University Medical Center, Rotterdam, the Netherlands
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Wouter A.S. Doff
1Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
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Peter Wever
3Jeroen Bosch Hospital, ‘s-Hertogenbosch, the Netherlands
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Khoa Thai
4Star-shl Diagnostic Laboratories, Rotterdam, the Netherlands
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Jeroen J. A. van Kampen
2Viroscience Department, Erasmus University Medical Center, Rotterdam, the Netherlands
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Bart L. Haagmans
2Viroscience Department, Erasmus University Medical Center, Rotterdam, the Netherlands
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  • ORCID record for Bart L. Haagmans
Jeroen A. A. Demmers
1Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
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  • ORCID record for Jeroen A. A. Demmers
  • For correspondence: j.demmers@erasmusmc.nl
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ABSTRACT

The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry based (MS) proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Manuscript now includes exciting novel data from COVID-19 patient cohorts.

  • https://www.ebi.ac.uk/pride/

  • List of abbreviations

    PRM
    parallel reaction monitoring
    AUC
    area under the curve
    nLC-MS
    nanoflow liquid chromatography – mass spectrometry
    Ct
    threshold value
    PCR
    polymerase chain reaction
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    Posted April 28, 2021.
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    Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens
    Karel Bezstarosti, Mart M. Lamers, Wouter A.S. Doff, Peter Wever, Khoa Thai, Jeroen J. A. van Kampen, Bart L. Haagmans, Jeroen A. A. Demmers
    bioRxiv 2020.04.23.057810; doi: https://doi.org/10.1101/2020.04.23.057810
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    Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens
    Karel Bezstarosti, Mart M. Lamers, Wouter A.S. Doff, Peter Wever, Khoa Thai, Jeroen J. A. van Kampen, Bart L. Haagmans, Jeroen A. A. Demmers
    bioRxiv 2020.04.23.057810; doi: https://doi.org/10.1101/2020.04.23.057810

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