Friday, January 31, 2020

PCR + Mass spectrometry for Coronavirus detection!

This study is a couple of years old, but it highlights a whole clever way of detecting pathogens  -- amplifying DNA and then doing mass spectrometry of the amplicons.

-You can start with virtually no DNA and make a ton of it
-MALDI-TOF is fast when you've got a ton of samples to screen
-MALDI instruments, while maybe not very common in research environments, are increasingly common in clinical labs. (Big question, though, is the flexibility -- I think that a lot of these are locked down to performing one specific assay, but -- still -- those places would have staff with the technical expertise to prep the samples and run the instruments
-If you pick primers well, you'd be resistint to mutations in the viral strains

-PCR takes time. Is it faster than it was?
-It takes some people a long time to make primers and to verify they don't cross-react. (I've heard tools have gotten better)
-MALDI is almost always connected to low power TOF devices (sensitivity, resolution and accuracy are the things that are typically the low part)

Check out this alternative technique that would alleviate some of this --

Same general idea -- 15 years ago -- this group amplified their virus DNA (SARS-coronavirus) and then did FTICR....are there a few thousand smaller, faster FTMS devices around the world right now? If you've already done PCR would you even need to couple it to HPLC? FIA-MS on an Orbitrap?

Sorry if you're tired of hearing about these viruses, but I'm motivated to read/write about it

On the topic of the 2019-nCOV (Wuhan) coronavirus -- check out this beautiful resource from NextStrain!

If you are working on this from a proteomics/mass spec/clinical detection perspective and want to talk, please reach out ( I'd be happy to lend a hand developing/troubleshooting assays or by (much more usefully) connecting you to people who could be of great assistance.

And -- while I'm sleepy rambling -- check this out -- ModPred ( thinks palmitoylation is a dominant PTM -- if you are developing peptide specific assays -- I'd skip that entire protein terminus.

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