Proteotyping SARS-CoV-2 virus from nasopharyngeal swabs: a proof-of-concept focused on a 3 min mass spectrometry window

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 immunodiagnostic that would not require specific reagents are worth 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. 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 results pave the way for the development of time-efficient viral diagnostic tests based on mass spectrometry.

A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research

“…To identify high quality tryptic virus peptides for use in targeted proteomics analyses, data-dependent acquisition (DDA) mass spectrometry was conducted on the mature SARS-CoV-2 virion. The Toronto SB3 virus strain 6 Together, these data confirm and expand upon previous proteomic analyses of SARS-CoV-2 virions, infected cells 4, 7-11 and patient samples [12][13][14] , and provide a library of high quality virus peptide spectra covering 17 virus proteins that can be used for the creation of peptide spectral libraries and targeted proteomics approaches.…”

A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry

“…Mass spectrometry (MS) based viral peptide detection has earlier been used for detection of viral proteins (Majchrzykiewicz-Koehorst et al 2015 ; Foster et al 2015 ; Santana et al 2014 ). Identification of SARS-CoV-2 specific peptides have also been reported recently (Gouveia et al 2020 ; IIhling et al 2020 ). Gouveia et al used SARS-CoV-2 infected cell lysate to identify peptides and validated these peptides in nasopharyngeal swab (Gouveia et al 2020 ).…”

Perspective on Proteomics for Virus Detection in Clinical Samples

“…This peptide belonging to the nucleoprotein has also been identified by DDA as a potential SARS-CoV-2 target with high abundance in purified virus preparations and nasopharyngeal swab samples. 10 It should be further highlighted that for clinical diagnostics a database tailored for clinical use cases makes more sense than including the whole UniProtKB into the analysis. This decreases the needed computational power and would have no negative effect on the false-positive rate in the real-world application of clinical diagnostics.…”