Supercharging Mass Spectrometry in the Fight Against SARS-CoV-2

By May 25, 2021

Waters’ latest product launch will supercharge the role of mass spectrometry research in the fight against SARS-CoV-2. Scientists can now directly quantify specific viral NCAP peptides in a highly reproducible manner with the Waters SARS-CoV-2 LC-MS Kit (RUO), allowing breakthrough research of the SARS-CoV-2 virus.


What role has Waters liquid chromatography and mass spectrometry played so far in the pandemic, and what has changed?

From the beginning of the COVID-19 pandemic, Waters has been committed to working with our customers and partners developing vaccines, researching therapeutics, and manufacturing PCR primers and probes used for testing. Waters established a COVID-19 Innovation Response Team to coordinate over 40 collaborations with dozens of customers and made significant in-kind donations and philanthropic gifts to organizations fighting the pandemic. Waters LC-MS systems have been used to:

Thus far, LC-MS has had a limited role in direct viral detection. While an LC-MS method for detection of peptides of SARS-Cov-2 proteins had been successfully demonstrated previously1, these studies also highlighted that the technique suffered from significant matrix effects due to interferences arising from the constituent components of the sample matrix, such as viral transport medium (VTM), limiting the analytical sensitivity of the methods. Not anymore!

The analytical sensitivity breakthrough: anti-peptide antibody enrichment

In order to address the issues affecting analytical sensitivity with other methods, Waters developed the SARS CoV-2 LC-MS Kit (RUO) based on research performed in collaboration with a coalition of academic, commercial, and government research scientists. This included inspirational collaborators from the University of Ghent2, the incredible team of researchers affiliated with the United Kingdom’s National Health Service (NHS)3, as well as other partners. The end result is a first-to-market, LC-MS-based end-to-end research solution to equip scientists with a reliable analytical method for the detection of SARS-CoV-2 signature peptides.

The analytical method enabled by the SARS CoV-2 LC-MS Kit (RUO), provides analytically sensitive, and analytically selective detection of viral peptides.

Analytical tests show that researchers can achieve the analytical sensitivity required to detect and quantify low levels of three unique peptides derived from the SARS CoV-2 NCAP protein – data on the Xevo™ TQ-XS system shows a lower limit of quantification (LLoQ) of just 3amol/µL (inter-day precision ≤17.4% CV, and intra-day precision ≤ 17.1%CV), compared to non-enriched research methods that show LLoQs of 220amol/µL. Results can be captured with clean, low-noise chromatograms in less than two minutes per sample.

The SARS CoV-2 LC-MS Kit (RUO) uses the innovative SISCAPA® anti-peptide antibody enrichment sample preparation method and antibodies from SISCAPA Assay Technologies, Inc. that improves the performance of mass spectrometry for measurement of pre-selected protein targets:

  • Greater analytical sensitivity through sample concentration and removal of interferences that suppress MS ionization of target peptides.
  • Faster LC-MS sample throughput through selective removal of background interference that would otherwise contribute to longer chromatographic run times. In conjunction with a 3 cm, 1.7 µm column, the LC-MS cycle time is now reduced to just 2.5 minutes per injection.
  • Improved LC-MS method robustness with extended column lifetimes and reduced instrument downtimes as a result of cleaner samples for injection.
  • The enrichment technique minimizes sample media interference, providing greater flexibility for the analysis of multiple research samples.


Waters’ end-to-end solution for direct SARS-CoV-2 signature peptide detection

For Research Only, not for use in Diagnostic Procedures. This Research Use Only kit has not been tested on clinical samples.

Waters’ SARS CoV-2 LC-MS Kit (RUO) has been optimized on the ACQUITY UPLC™ I-Class System, and the Xevo™ TQ-XS Detector. It comes in an adaptable automation-friendly format with liquid handling protocols for the Andrew+ Pipetting Robot on OneLab™ Software. To ensure reproducible quantitation and minimize the risk of nonspecific binding of peptides to surfaces, the SARS CoV-2 LC-MS Kit (RUO) employs QuanRecovery™ Plates with MaxPeak™ HPS and a MaxPeak Premier Column.

The accompanying Instructions for Use detail the correct utilization of the kit, and the Scientific Application Note:  Advancing Research with the SARS-CoV-2 LC-MS Kit (RUO) shows the analytical sensitivity of the method as evaluated by Waters’ Clinical Scientific Operations group over three runs at 2, 3, 6, 10 and 20 amol/µL synthetic peptides spiked into VTM.


Isn’t PCR the “Gold Standard”? Why should I care about viral peptides?

Not enough can be said about the role that PCR techniques have played in the world’s response to the COVID-19 pandemic – hundreds of millions of tests performed, and countless infections prevented due to the high sensitivity of these tests. PCR tests are and will likely continue to be essential in the diagnosis of COVID-19 and many other infectious diseases. However, we should not overlook some of the discovered issues due to the wide usage of PCR during the pandemic:

  • PCR tests use the polymerase chain reaction to replicate specific segments of SARS-CoV-2 RNA consecutively until there are enough copies for a detector to sense. Studies have shown4 that a patient’s cells may continue to shed viral RNA5 long after that patient is no longer considered infectious – sometimes months afterwards6 – potentially leading to situations where patients continue to test positive with PCR tests and may be required to remain in quarantine despite no longer posing a threat of infecting others. As seen in this article published in Nature, Viral peptides appear in the body in a narrower window than RNA, and are more closely tied to the infectious period7, thus, a highly sensitive and highly selective viral peptide detection method might be a valuable and complementary research tool.
  • It is well known that despite their high sensitivity, quantitative PCR tests often show high variability8, even between runs within the same lab, and between the same test run at different labs. This has been shown for SARS-CoV-2 PCR Tests as well, here9 and here3.  LC-MS utilizes calibration curves and Stable Isotope-Labelled standards to ensure reproducibility and consistency across labs, and provides a direct measurement of the target analytes without the need to create millions of copies – potentially making it an important tool for longitudinal research studies across labs and at different points in time.
  • Supply Chain: It was well documented, particularly early during the pandemic and into the summer of 2020, that there were many cases of localized PCR reagent, and lab consumable shortages10. If a new virus with unique targets emerges in the future, it is possible that the world would once again experience shortages as the supply catches up to the demand of the requisite consumables and reagents. Even quite recently, with India’s resurgence in SARS-CoV-2 infection, there are reports of localized PCR reagent shortages11 affecting the country’s ability to control the pandemic. In preparation for a future pandemic, enabling research on a wider array of technologies, thus diversifying the supply chain, might help relieve the constraints experienced by many labs.

Our motivation: enabling life-saving research

Our mission to continuously Deliver Benefit to our customers, employees, shareholders, and society at every opportunity, and our unwavering commitment to fight the SARS-CoV-2 pandemic has motivated us throughout the development of the Waters SARS-CoV-2 LC-MS Kit (RUO). Like many of our customers and partners around the world, the team behind this product launch has been directly impacted by the devastating effects of the pandemic. We take immense pride in empowering our customers with the tools to advance life-saving research and supercharge the potential of LC-MS in the fight against SARS-CoV-2.

Register Now for our COVID-19 Pandemic Mass Spectrometry Webinar: Advancing Research with the SARS-CoV-2 LC-MS Kit (RUO)  (11 a.m. EDT | 5 p.m. CEST on June 10, 2021)

Join Dominic Foley and the Waters Clinical Scientific Operations Team to understand how the SARS-CoV-2 LC-MS Kit (RUO) allows for the quantification of viral proteins to advance research of COVID-19.


Additional information and resources:


Have an idea, question, or collaborative proposal? We want to hear from you! If you don’t yet know your local Waters contacts, connect with the COVID Innovation Response Team for a scientific inquiry or to propose a collaboration.



  1. Cardozo, K.H.M., Lebkuchen, A., Okai, G.G. et al. Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun 11, 6201 (2020).
  2. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients, JACS Au Article ASAP (2021); DOI: 10.1021/jacsau.1c00048
  3. Lecture by Donald Jones of the University of Leicester during the second e-NVMS meeting on Covid-19 research of April 16th, 2021
  4. Lu J, Peng J, Xiong Q, Liu Z, Lin H, Tan X, et al. Clinical, immunological and virological characterization of COVID-19 patients that test re-positive for SARS-CoV-2 by RT-PCR. EBioMedicine. 2020;59. 2020
  5. Liguo Zhang, Alexsia Richards, M. Inmaculada Barrasa, Stephen H. Hughes, Richard A. Young, Rudolf Jaenisch. Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues. Proceedings of the National Academy of Sciences May 2021, 118 (21) e2105968118; DOI: 10.1073/pnas.2105968118
  6. N. Li, X. Wang, T. Lv. Prolonged SARS-CoV-2 RNA shedding: not a rare phenomenon. J. Med. Virol., 92 (11) (2020), pp. 2286-2287
  7. Mercer, T.R., Salit, M. Testing at scale during the COVID-19 pandemic. Nat Rev Genet (2021).
  8. Hayden RT, Yan X, Wick MT, et al. Factors contributing to variability of quantitative viral PCR results in proficiency testing samples: a multivariate analysis. J Clin Microbiol. 2012;50(2):337-345. doi:10.1128/JCM.01287-11
  9. Daniel Rhoads, David R Peaper, et al., College of American Pathologists (CAP) Microbiology Committee Perspective: Caution Must Be Used in Interpreting the Cycle Threshold (Ct) Value, Clinical Infectious Diseases, Volume 72, Issue 10, 15 May 2021, Pages e685–e686, DOI:10.1093/cid/ciaa1199
  10. American Society for Microbiology: Supply Shortages Impacting COVID-19 and Non-COVID Testing
  11. Kumar, Krishna. Now, shortage of RT-PCR kits adds to Maharashtra’s Covid-19 woes. Economic Times. 10 April 2021.

SISCAPA® is a mark of Anderson Forschung Group LLC (AFG).

Categories: COVID-19, Technologies