Friday, November 10, 2023

Circadium protein atlas (in mice) across 8 organs!


Circadium rhythm (is that spelled right? I bet it isn't. ryhthm? meh...) has been heavily investigated by transcript abundance, but we all know that measuring transcript abundance is 

This group knocked out two of the main circadian yrhtymhy proteins and then actually measured the things that people care about --> over 11,000 proteins! 

They made an easy resource that is almost as hard for a dysgraphic guy to spell at rhthym. You can find it here:

I have to admit I don't understand what the numbers mean under every protein that I've looked up in it, but I assume it'll make sense to people who know about circadium thrymrhths. 

The quan was done by isobaric tagging and a crapload of fractionation with LCMS on an Orbitrap HF or HF-X system. Curiously, the HF doesn't appear to have gotten the "TMT mode" upgrade to allow 45,000-ish resolution, but the HF-X did. So part of the files were analyzed at 60,000 resolution MS/MS while part were done at 45,000. If the authors see this, I was pretty sure that was a free upgrade? In my hands the HF and HF-X pretty much perform the same unless you are going to low loads. I think that at the amount on column here if the resolutions were matched the data would be about identical between the two, particularly when using a 100ms ion injection time. 

I wonder if they traded in the HF part way through the study and got an HF-X?  I need another coffee. I don't remember what I was even typing about. Oh, and they used a 0.7 Th isolation window in both experiments. 

Data processing was done with Proteome Discoverer and I think they really should have provided a citation for it, like this one. 😇 

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