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Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients

Bart Van Puyvelde (UGent) , Katleen Van Uytfanghe (UGent) , Olivier Tytgat (UGent) , Laurence Van Oudenhove, Ralf Gabriels (UGent) , Robbin Bouwmeester (UGent) , Simon Daled (UGent) , Tim Van Den Bossche (UGent) , Pathmanaban Ramasamy (UGent) , Sigrid Verhelst (UGent) , et al.
(2021) JACS AU. 1(6). p.750-765
Author
Organization
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 15 academic laboratories 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 other laboratories 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. Data are available via ProteomeXchange with identifier PXD022550.
Keywords
SARS-CoV-2, Mass Spectrometry, Proteomics, Viral Proteins, Diagnostics, MRM, QUANTIFICATION

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MLA
Van Puyvelde, Bart, et al. “Cov-MS : A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients.” JACS AU, vol. 1, no. 6, 2021, pp. 750–65, doi:10.1021/jacsau.1c00048.
APA
Van Puyvelde, B., Van Uytfanghe, K., Tytgat, O., Van Oudenhove, L., Gabriels, R., Bouwmeester, R., … Dhaenens, M. (2021). Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients. JACS AU, 1(6), 750–765. https://doi.org/10.1021/jacsau.1c00048
Chicago author-date
Van Puyvelde, Bart, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Robbin Bouwmeester, Simon Daled, et al. 2021. “Cov-MS : A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients.” JACS AU 1 (6): 750–65. https://doi.org/10.1021/jacsau.1c00048.
Chicago author-date (all authors)
Van Puyvelde, Bart, Katleen Van Uytfanghe, Olivier Tytgat, Laurence Van Oudenhove, Ralf Gabriels, Robbin Bouwmeester, Simon Daled, Tim Van Den Bossche, Pathmanaban Ramasamy, Sigrid Verhelst, Laura De Clerck, Laura Corveleyn, Sander Willems, Nathan Debunne, Evelien Wynendaele, Bart De Spiegeleer, Péter Judák, Kris Roels, Laurie De Wilde, Peter Van Eenoo, Tim Reyns, Marc Cherlet, Emmie Dumont, Griet Debyser, Ruben t’Kindt, Koen Sandra, Surya Gupta, Nicolas Drouin, Amy Harms, Thomas Hankemeier, Donald J. L. Jones, Pankaj Gupta, Dan Lane, Catherine S. Lane, Said El Ouadi, Jean-Baptiste Vincendet, Nick Morrice, Stuart Oehrle, Nikunj Tanna, Steve Silvester, Sally Hannam, Florian C. Sigloch, Andrea Bhangu-Uhlmann, Jan Claereboudt, N. Leigh Anderson, Morteza Razavi, Sven Degroeve, Lize Cuypers, Christophe Stove, Katrien Lagrou, Geert A. Martens, Dieter Deforce, Lennart Martens, Johannes P. C. Vissers, and Maarten Dhaenens. 2021. “Cov-MS : A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients.” JACS AU 1 (6): 750–765. doi:10.1021/jacsau.1c00048.
Vancouver
1.
Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, et al. Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients. JACS AU. 2021;1(6):750–65.
IEEE
[1]
B. Van Puyvelde et al., “Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients,” JACS AU, vol. 1, no. 6, pp. 750–765, 2021.
@article{8713802,
  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 15 academic laboratories 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 other laboratories 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. Data are available via ProteomeXchange with identifier PXD022550.}},
  author       = {{Van Puyvelde, Bart and Van Uytfanghe, Katleen and Tytgat, Olivier and Van Oudenhove, Laurence and Gabriels, Ralf and Bouwmeester, Robbin and Daled, Simon and Van Den Bossche, Tim and Ramasamy, Pathmanaban and Verhelst, Sigrid and De Clerck, Laura and Corveleyn, Laura and Willems, Sander and Debunne, Nathan and Wynendaele, Evelien and De Spiegeleer, Bart and Judák, Péter and Roels, Kris and De Wilde, Laurie and Van Eenoo, Peter and Reyns, Tim and Cherlet, Marc and Dumont, Emmie and Debyser, Griet and t’Kindt, Ruben and Sandra, Koen and Gupta, Surya and Drouin, Nicolas and Harms, Amy and Hankemeier, Thomas and Jones, Donald J. L. and Gupta, Pankaj and Lane, Dan and Lane, Catherine S. and El Ouadi, Said and Vincendet, Jean-Baptiste and Morrice, Nick and Oehrle, Stuart and Tanna, Nikunj and Silvester, Steve and Hannam, Sally and Sigloch, Florian C. and Bhangu-Uhlmann, Andrea and Claereboudt, Jan and Anderson, N. Leigh and Razavi, Morteza and Degroeve, Sven and Cuypers, Lize and Stove, Christophe and Lagrou, Katrien and Martens, Geert A. and Deforce, Dieter and Martens, Lennart and Vissers, Johannes P. C. and Dhaenens, Maarten}},
  issn         = {{2691-3704}},
  journal      = {{JACS AU}},
  keywords     = {{SARS-CoV-2,Mass Spectrometry,Proteomics,Viral Proteins,Diagnostics,MRM,QUANTIFICATION}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{750--765}},
  title        = {{Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients}},
  url          = {{http://dx.doi.org/10.1021/jacsau.1c00048}},
  volume       = {{1}},
  year         = {{2021}},
}
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