The Mass Spec COVID Check

Rising population density, global mobility, and insufficient health care in poor countries all contributed to the rapid spread of COVID-19. Testing is crucial to fight the SARS-CoV-2 virus, and now is the time to prepare for future outbreaks. It’s my view that MS could be employed to provide faster and cheaper diagnosis in the case of such events.

Diagnostic tests recognize unique molecular signatures from pathogens. These may take the form of small molecules or macromolecules (nucleic acid chains, proteins, carbohydrates, or lipids). DNA and RNA represent obvious targets because of our long-standing ability to amplify signals by PCR. Millions of PCR-based tests are performed each day. Although these are efficient, automatable, and acceptably cheap, the world cannot rely on one technology alone. Not only are reagents in short supply, but the test is also difficult to validate, and false results (positive and negative) may go undetected.

There is a need for an orthogonal diagnostic test that targets a different biomolecule. Like many other viruses, SARS-CoV-2 produces virus-like particles (VLPs) that contain proteins, but no RNA. These are attractive targets, and have been historically targeted using antibodies. However, these antibodies are expensive – and they come in various flavors that each yield slightly different results.

So we set out to analyze SARS-CoV-2 proteins by MS. Within two weeks, we had identified 17 peptides that were readily detected from nasal swabs by clinically applicable tandem quadrupole instruments. Sample preparation for protein detection is faster (taking less than 20 minutes) and cheaper (using under $5 worth of reagents) than that for RNA (which takes hours and costs $20 to $30 per sample), and it uses readily available reagents. Tandem quadrupole MS is also in routine use in the clinic – these instruments can be found in academic and industrial settings in cities around the world.

But MS instruments are much more diverse than quantitative PCR instruments, which complicates method standardization. To address this issue, we approached the challenge as a community, seeking help from MS vendors (including the Waters Corporation’s COVID-19 Innovation Response Team and Sciex), as well as over a dozen academic labs in a consortium called Cov-MS. By providing them with an SOP – an open-source software template containing all the target peptides (Skyline) and a sample kit containing recombinant viral proteins – these groups were able to efficiently select the best targets for analysis. In parallel, we also analyzed patient samples. We showed that protein signal intensity correlates well with diagnostic (Ct) values ​​from PCR-based tests. MS may thus make a valuable addition to the short-term testing toolbox.

Two main challenges remain. First, MS samples must be measured consecutively instead of in parallel. Our current analyses take eight minutes per sample, but Cov-MS consortium members at Alderley Analytical have achieved this in two minutes – this could mean over 700 patient samples a day! Acoustic Ejection MS could then increase this number to tens of thousands of patient samples a day. The second challenge is increasing sensitivity. We can already detect patient samples down to a Ct value of 25, but we believe that this sensitivity could be improved by up to four orders of magnitude using innovative enrichment approaches, such as peptide immunoprecipitation.

No one knows for sure when an MS-based test will be ready for the clinic, or even when the clinic will be ready for MS. But collaboration and data sharing is needed if MS is to rival PCR in terms of output and scale. Not trying would be nothing short of negligent.