Wednesday, October 30, 2019

Transcript Abundance IS NOT THE SAME as protein abundance!

It's 2019....and I'm shocked that this even needs to be said to anyone, but it does. I know it doesn't have to be said to the brilliant people who, for some reason, come to this blog to read my rambling about proteomics, but -- hey -- maybe my annoyed rambling here will actually be useful to someone!

Here we go:

Transcript abundance does not correlate with protein abundance.

I'm going to throw in proof that I filtered on one criteria -- "does it say it in the title or abstract?" because the people you're going to need to say this to probably aren't reeeaaaal into reading. Heck, I'll even highlight it.

#1 It can, if you go on a gene by gene basis (and organism by organism) and throw in adjustment factors.

#2 --- Maybe this is a new finding?  HINT: IT ISN'T!!!

In 2009, these authors suggest that you basically keep a list (it's going to be small) of the proteins where RNA abundance and protein abundance correlate. THEN you can trust the mRNA levels to be helpful for predicting protein abundance.

#3) Who's heard of these journals? Let's look at a really thoughtful review in something called Call? Sell?

I'm not even trying, yo. For real. I did a SILAC experiment (the gold standard for protein quantification) and RNA Microarrays on the same samples way way way back in the day. 1% overlap. Yes -- on an Orbitrap XL with SCX fractionation, I didn't get close to complete proteome coverage. I was PUMPED by a few thousand with quan. And microarrays died out for a very good reason (or should have, if they haven't).

1% overlap in quan. system was messed up...but, come one. You'd think by chance it would be better.

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