Proteotyping SARS-CoV-2 Virus from Nasopharyngeal Swabs: A Proof-of-Concept Focused on a 3 Min Mass Spectrometry Window

Journal of Proteome Research
D. GouveiaJean Armengaud

Abstract

Rapid but yet sensitive, specific, and high-throughput detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is key to diagnose infected people and to better control the spread of the virus. Alternative methodologies to PCR and immunodiagnostics that would not require specific reagents are worthy to investigate not only for fighting the COVID-19 pandemic but also to detect other emergent pathogenic threats. Here, we propose the use of tandem mass spectrometry to detect SARS-CoV-2 marker peptides in nasopharyngeal swabs. We documented that the signal from the microbiota present in such samples is low and can be overlooked when interpreting shotgun proteomic data acquired on a restricted window of the peptidome landscape. In this proof-of-concept study, simili nasopharyngeal swabs spiked with different quantities of purified SARS-CoV-2 viral material were used to develop a nanoLC-MS/MS acquisition method, which was then successfully applied on COVID-19 clinical samples. We argue that peptides ADETQALPQR and GFYAQGSR from the nucleocapsid protein are of utmost interest as their signal is intense and their elution can be obtained within a 3 min window in the tested conditions. These resul...Continue Reading

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Citations

Oct 18, 2020·Nature Communications·Subash AdhikariMark S Baker
Nov 26, 2020·Proteomics·Lucia Grenga, Jean Armengaud
Dec 5, 2020·Nature Communications·Karina Helena Morais CardozoValdemir Melechco Carvalho
Nov 10, 2020·Journal of Proteins and Proteomics·Rashmi RanaNirmal Kumar Ganguly
Feb 20, 2021·Journal of Proteome Research·Wout BittremieuxNuno Bandeira
Dec 1, 2020·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Shikha ThakurGaurav Joshi
May 7, 2021·Analytical Chemistry·George P AndersonEllen R Goldman
Jun 6, 2021·Molecular & Cellular Proteomics : MCP·Jeremy L Praissman, Lance Wells
May 18, 2021·Trends in Analytical Chemistry : TRAC·Justin H Griffin, Kevin M Downard
Jul 23, 2021·Journal of Proteome Research·Dong-Gi MunAkhilesh Pandey
Dec 5, 2020·Analytical Chemistry·Tobias P WörnerAlbert J R Heck
Aug 26, 2021·Journal of Proteome Research·Marica GrossegesseAndreas Nitsche
Oct 23, 2020·Journal of Proteome Research·Marica GrossegesseThilo Muth
Sep 4, 2021·Analytical Biochemistry·Hoda IlkhaniSiamak Farhad

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Datasets Mentioned

BETA
MT066156
PXD019686

Methods Mentioned

BETA
proteotyping
FCS
electrophoresis
deamidation
PCR
targeted
proteomics assay

Software Mentioned

MASCOT Daemon
Unipept
MASCOT
Matrix Science

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