Dataset Information

Cov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patients

ABSTRACT: Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by Reverse Transcription Polymerase Chain Reaction (RT-PCR). Although this is efficient, automatable and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We, therefore, developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using Mass Spectrometry (MS). We established the Cov-MS consortium, consisting of fifteen academic labs and several industrial partners to increase applicability, accessibility, sensitivity and robustness of this kind of Sars-Cov-2 detection. This in turn gave rise to the Cov-MS Digital Incubator that allows labs to join the effort, navigate and share their optimizations, and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR, using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments.

INSTRUMENT(S): TripleTOF 5600, TripleTOF 6600

ORGANISM(S): Sars Coronavirus Cdc#200301157 Homo Sapiens (human)

DISEASE(S): Covid-19

SUBMITTER: Maarten Dhaenens

LAB HEAD: Maarten Dhaenens

PROVIDER: PXD022550 | Pride | 2021-07-16

REPOSITORIES: pride

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			Action	DRS
	200328_Sciex5600_S63879_1.wiff	Wiff
	200328_Sciex5600_S63879_1.wiff.scan	Wiff
	200328_Sciex5600_S63879_11.wiff	Wiff
	200328_Sciex5600_S63879_11.wiff.scan	Wiff
	200328_Sciex5600_S63879_13.wiff	Wiff

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Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients.

Van Puyvelde Bart B Van Uytfanghe Katleen K Tytgat Olivier O Van Oudenhove Laurence L Gabriels Ralf R Bouwmeester Robbin R Daled Simon S Van Den Bossche Tim T Ramasamy Pathmanaban P Verhelst Sigrid S De Clerck Laura L Corveleyn Laura L Willems Sander S Debunne Nathan N Wynendaele Evelien E De Spiegeleer Bart B Judak Peter P Roels Kris K De Wilde Laurie L Van Eenoo Peter P Reyns Tim T Cherlet Marc M Dumont Emmie E Debyser Griet G t'Kindt Ruben R Sandra Koen K Gupta Surya S Drouin Nicolas N Harms Amy A Hankemeier Thomas T Jones Donald J L DJL Gupta Pankaj P Lane Dan D Lane Catherine S CS El Ouadi Said S Vincendet Jean-Baptiste JB Morrice Nick N Oehrle Stuart S Tanna Nikunj N Silvester Steve S Hannam Sally S Sigloch Florian C FC Bhangu-Uhlmann Andrea A Claereboudt Jan J Anderson N Leigh NL Razavi Morteza M Degroeve Sven S Cuypers Lize L Stove Christophe C Lagrou Katrien K Martens Geert A GA Deforce Dieter D Martens Lennart L Vissers Johannes P C JPC Dhaenens Maarten M

JACS Au 20210503 6

Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automa ...[more]

PMID: 34254058

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Project description:There is an urgent need for robust and high-throughput methods for SARS-CoV-2 detection in suspected pa-tient samples to facilitate disease management, surveillance, and control. Although nucleic acid detection methods such as RT-PCR are the gold standard, during the current pandemic the deployment of RT-PCR tests has been extremely slow, and key reagents such as PCR primers, and RNA extraction kits are at critical shortages. Rapid point-of-care viral antigen detec-tion methods have been previously employed for the diagnosis of respiratory viruses such as influenza and respiratory syn-cytial viruses. Therefore, the direct detection of SARS-CoV-2 viral antigens in patient samples could also be used for diagno-sis of active infection and alternative methodologies for specific and sensitive viral protein detection should be explored. Targeted mass spectrometry techniques have enabled the identification and quantitation of a defined subset of pro-teins/peptides at single amino acid resolution with attomole level sensitivity and high reproducibility. Herein we report a tar-geted mass spectrometry assay for the detection of SARS- CoV-2 spike protein and nucleoprotein in a relevant biologi-cal matrix. Recombinant full-length spike protein and nucleoprotein were digested and prototypic peptides were selected for parallel reaction monitoring (PRM) quantitation using a high resolution Orbitrap instrument. A spectral library, which con-tained 7 proteotypic peptides (4 from spike protein and 3 from nucleoprotein) and the top 3 to 4 transitionsMS2 spectra, was generated and evaluated. From the original spectral library, we selected 2 best performing peptides for the final PRM assay. The assay was evaluated using mock test samples containing inactivated SARS-CoV-2 virions, added to in-vitro de-rived mucus. The PRM assay provided a limit of detection (LOD) of ~200 attomoles and a limit of quantitation (LOQ) of ~ 390 attomoles. Extrapolating from the test samples, the projected titer of virus particles necessary for detection of SARS-CoV-2 spike and nucleoprotein detection was approximately 2E5 viral particles/mL, making it an attractive alternative to RT-PCR assays. Potentially mass spectrometry-based methods for viral antigen detection may deliver higher throughput and could serve as a complementary diagnostic tool to RT-PCR. Furthermore, this assay could be used to evaluate the pres-ence of SARS-CoV-2 in archived or recently collected biological fluids, in-vitro derived research materials, and wastewater samples