Tuesday, November 1, 2022

Run your TIMSTOF smarter with SliceDIA!

Edits, 11/2/2022. I continually forget that people outside of a close knit group of weirdos read this blog, and I still don't know why.

I also tend to forget that there are human beings behind some of these products and that if I'm going to stick to a rule where I only post paper that I can say nice things about, I should consider doing that for products. Being a grown-up is dumb. I have to wear SLACKS today and adult shoes. 

As such, I'm going to edit this post somewhat. 

If you've ever had the opportunity to look at a TIMSTOF up close you've probably thought something like "how could the technology behind this be so powerful to justify the headaches of feeling like you're back at being an early adopter again. 

But that's the thing, behind these instruments that have a long way to go in terms of accessibility to new users (the captivespray source can be really tough for new people) and a data format that still doesn't play well with much at all, you have this unbelievable potential that somehow makes it worth the frustration. (It isn't as bad as the SLED9X official format). 

A running joke is that literally no one knows what happens when you change any settings in pasefDIA. Florian Meier came up with a method and we all use it and there are 7 pages of settings that literally no one knows what they do. 

What if there is a better way? 

Introducing the SLICING DIAICING most powerful way to run one of these giant things anyone has come up with yet! 


Worried about a TIMSTOF literally falling over if you try this, and it had better be worth it for you to even consider it? 

200 picogram "single cell loads" 

On an EvoSep running the 200 sample per day method (microflow!) -- that's like 7 minutes. (24x60/200?)

1,400 proteins per tip on a TIMSTOF Pro2 (not an SCP or HT) in 7 minutes??

Now, calling 200 picograms of peptide the equivalent of single cell is something we can argue about later. 

Nevermind, we can argue about it now. If there is 200 picograms of PROTEIN in a normalish human cell, you'd need 100% extraction efficiency, 100% digestion efficiency, and zero peptide adherence to anything to get to 200 picograms of peptide. Not one of those things is remotely possible. 

But since it makes a decent fictional benchmark for the emerging field of single cell proteomics and that is what everyone is doing, this is still absolutely insane in terms of IDs and coverage and better than anything we've ever seen.

See! I can clean this up.

Setting SLICEDIA up is really easy! And the data output while it is running looks super crazy! 

I'll upload methods for the Flex and SCP shortly. 

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