Thursday, March 26, 2020

Another day -- another great COVID-19 proteomics study!

Who knew proteomics was so fast?!?! COVID-19 study number 3?!?

I was thrown off at first because I didn't recognize the species in their FASTA files. The SARS-CoV-2 virus was used to infect monkey cells.

Nanopore sequencing was used here as well as "high-low" shotgun proteomics on a Fusion Lumos system.
(High resolution MS1, ultra fast, low resolution MS/MS in the ion trap. I'm pretty sure they used HCD fragmentation. (I don't have time to go back through it today).

What I did think was interesting enough to screenshot was the number of phosphorylation sites that the detected. I know I rambled about the ModPred program on here somewhere recently (Edit -found it!)  and, check this out!

I can't use pictures from the preprint due to the copyright terms, but the phosphorylation sites that they find line up surprisingly well with the ModPred predictions!

There is a neat point where they find multiple phosphorylation sites in one area that ModPred is convinced there is only one likely location....and given that it is ion trap data, it wouldn't be strange to think that the localization was difficult. It would be interesting to take a deeper look into which one was right in that scenario.

The RAW files have been publicly uploaded, but I can't seem to pull them down. They are through a service I haven't heard of before.

No comments:

Post a Comment