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

Karel Bezstarosti; Mart M. Lamers; Wouter A.S. Doff; Peter C. Wever; Khoa T.D. Thai; Jeroen J.A. van Kampen; Bart L. Haagmans; Jeroen A.A. Demmers

doi:10.1371/journal.pone.0259165

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

Karel Bezstarosti, Mart M. Lamers, Wouter A.S. Doff, Peter C. Wever, Khoa T.D. Thai, Jeroen J.A. van Kampen, Bart L. Haagmans, Jeroen A.A. Demmers^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

26 Citations (Scopus)

25 Downloads (Pure)

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 (MS) based 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 estimated to be 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.

Original language	English
Article number	e0259165
Journal	PLoS ONE
Volume	16
DOIs	https://doi.org/10.1371/journal.pone.0259165
Publication status	Published - 11 Nov 2021

Bibliographical note

Publisher Copyright:
© 2021 Bezstarosti et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Access to Document

10.1371/journal.pone.0259165

journal.pone.0259165Final published version, 2.08 MBLicence: CC BY

Cite this

@article{c8c905ef48fb408099356c68962bd684,

title = "Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens",

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 (MS) based 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 estimated to be 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.",

author = "Karel Bezstarosti and Lamers, {Mart M.} and Doff, {Wouter A.S.} and Wever, {Peter C.} and Thai, {Khoa T.D.} and {van Kampen}, {Jeroen J.A.} and Haagmans, {Bart L.} and Demmers, {Jeroen A.A.}",

note = "Publisher Copyright: {\textcopyright} 2021 Bezstarosti et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",

year = "2021",

month = nov,

day = "11",

doi = "10.1371/journal.pone.0259165",

language = "English",

volume = "16",

journal = "PLoS ONE",

issn = "1932-6203",

publisher = "Public Library of Science",

}

TY - JOUR

T1 - Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens

AU - Bezstarosti, Karel

AU - Lamers, Mart M.

AU - Doff, Wouter A.S.

AU - Wever, Peter C.

AU - Thai, Khoa T.D.

AU - van Kampen, Jeroen J.A.

AU - Haagmans, Bart L.

AU - Demmers, Jeroen A.A.

N1 - Publisher Copyright: © 2021 Bezstarosti et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2021/11/11

Y1 - 2021/11/11

N2 - 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 (MS) based 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 estimated to be 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.

AB - 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 (MS) based 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 estimated to be 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.

UR - http://www.scopus.com/inward/record.url?scp=85119019382&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0259165

DO - 10.1371/journal.pone.0259165

M3 - Article

C2 - 34762662

AN - SCOPUS:85119019382

SN - 1932-6203

VL - 16

JO - PLoS ONE

JF - PLoS ONE

M1 - e0259165

ER -

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

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this