Monday, March 21, 2022

Prioritized target selection improves reproducibility in (anything) and single cell proteomics!


There's a lot here and I am in the middle of a single cell prep, so I have to move fast.

What is it? More proof of what having single cell proteomics as a moonshot project can do for everything! 

Here is the preprint:

Whoa. That's a lot of names! 

Are you super tired of single cell proteomics and did single mouse macrophages just make you vomit in your mouth a little? I get it, but you know that whole "proteomics isn't reproducible" thing that has followed us from the first QTOFs and won't seem to go away?

MaxQuant.Live targeting is a really smart step in the right direction. What it lets you do is make a crazy huge list of targets (25,000 is realistic) and fragment those things in just about every run. But what if you don't have enough cycle time to get to everything that you want to? That happens. Heck, I'd prefer to just fragment every peptide from every human protein every time, but I can't yet (....DIA people...sorry, I ain't there yet). What if now you could prioritize your targets. 

It's sort of like using a targeted list on the Q Exactive and then checking that little box waaaaaaaay down at the bottom that says something like "if idle...pick others", but imagine that you've got tiers. And real time retention time alignment. And you went ahead and built your target list and retention times automatically off of a DIA run. Then you've got a handle on what this is. 

If you're thinking....meh...that's cool, but I don't have a million dollars right this second? How 'bout not a goshdarned thing? 

You do need MaxQuant.Live 2.1, but it isn't quiiiiiiiiiiiiiiiiiiite ready yet. I found 3 links in the paper and one that did this... what we're currently running is 2.0.3, I think

Now, this is where the plot thickens. 2.0.3 works for all Q Exactives (actually, I've never tried a Focus or a UHMR, but I've installed it on everything else)  and Exploris series instruments, but check out this statement: 

If true (this is a preprint, of course) this could be really great for a lot of people out there who wouldn't mind a little more reproducibility out of a venerable instrument! 

Back to the paper, this group does some really impressive single cell proteomics using this approach and reading through that will take more time than I have. I'll keep hitting the refresh button on the MaxQuant.Live webpage and let you know when I see a new link! 

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