Thursday, March 12, 2020

CoVID-19 / SAR-CoV-2 infected cells real proteomics data!!

Not a proteomics expert and just want to see what happens to protein expression during COVID-19 infection? Here is this amazing web portal that went live this morning! 

Significance statement (if you're not sure why COVID-19 is significant, please go back under your rock) but also -- keep in mind that proteins from these  viruses become detectable in body fluids BEFORE symptoms appear.

2003 SARS Paper showing this is the case in that disease
medRXiV on CoVID-19 that posted yesterday that supports all of this!

Begin standard rambly proteomics blog post:

Remember when the 2003 SARS thing happened and we were useless? With one scan per second and instruments that could just almost detect protein in solution that you could see with the naked eye, mass spectrometry was a medical curiosity. (It didn't stop people from running around saying bold things and building expectations that we couldn't meet, the fallout of which we're all still dealing with now).

NOW --- We can help. It might take some sleep deprivation from a really truly skilled team. And here is proof.

Interested in coronavirus, what it does to the proteome of infected cells, and what different drugs do to it?

I'm not even kidding. They did all this stuff and more resources have gone live since it posted last night.

Here is a link to the RAW files.

Want to interrogate individual proteins -- online? Here is their website!

Edit: And this isn't some crappy rush job. This data is superb. The loading is well controlled, the gradients look great and there is a good balance in the MS2 between the reporter ion liberation and the peptide fragment ions -- I don't have it all downloaded yet, but what I do looks like this ---

-- we don't want to be dealing with a pandemic, but if one was going on these are the kinds of people we want and need out there working on it.

Shameless plug: We've been trying to make peptide/protein detection assays available for as many LCMS systems as we can . We know this resource isn't perfect -- heck, it might not even be good, but we're trying to make resources that are helpful. Another draft is in works with some corrections and updates, but we have to sleep sometime. Here is the first draft preprint.

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