Thursday, April 13, 2023

Western blots are still dumb.

 I know I'm preaching to the choir, and maybe this isn't my first rant....

...or my second...

But I was reading this new study this morning

on a drug that I've been messing with for a little over a year and in every single cell line I've dosed with the drug, I've seen a decreased abundance of the ERK protein of 2-5 fold.

By DDA, by DIA, whatever, there is always less of this protein when I dose my ATCC cell lines with this drug. 

Sure doesn't look like the case by Western blot.... The 2-fold doesn't surprise me, what I tell students is that if you see it 5-fold different by LCMS, you can "validate" that by Western. I haven't used these cell lines, but I'm curious now and will get them.

Here is the thing, though, if you go through this study almost every figure and result in this study focuses on whether ERK and/or phospho-ERK are altered by single/double drug/ siRNA, whatever, treatment. 

What does this do to the rest of a very nice study if there really is a significant alteration in your protein levels/abundances and you just can't see it? If I go through this paper and assume every time they see ERK unaltered, it actually is, then EVERY conclusion of this nice looking (and obviously difficult) study needs questioned, if not completely thrown out. 

Considering this might be the single most promising drug ever developed for pancreatic cancer, I'd really prefer if the measurements were a little more accurate. 

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