Monday, August 22, 2022

Super expert TMT Post #2 : How to mix plexes by Alejandro Brenes!

 See post #1 yesterday, but if coming from somewhere outside this blog. Here is the link

This original paper has appeared on the blog at some point, for sure, maybe twice because it is amazing. But it should be posted here again because it is such an important topic

The original paper provides advice for how to mix different plexes, what to definitely avoid and has all the math to back up the fact they are not making this up! 

Why post it again? When this paper was submitted the TMTPro18 reagents weren't yet out. Rather than making you wait for him to wrap up his thesis and find it (I'm sure it will be worth reading!) he made the updated diagrams available for these reagents! 

Higher resolution is available here (I can't embed twitter's new .jiffyjaff format or whatever it is in blogger. Off topic, but Amazon now uses a new image format for everything, including your personal images if you use their cloud backup thingy. I can't embed those either.)

I bugged him about my own personal issues with medium resolution instruments and multiplexing (on the TIMSTOF and 7600 we can only 10-plex using 126, 135 and 127-134 and he made this as well (you can find the higher res in the same Tweeter thread in the link above).  

It is funny because just a couple of years ago when we were limited to 10-plex on ultra high res instruments, a lot of people independently decided that combining plexes wasn't worth it. CPTAC plowed on combining plexes leaving the quiet implication on the table that maybe we should read their papers in their entirety rather than just working through to figure out just how much one of these amazingly expertly analyzed tumor samples cost on average. (Whoever said this last round cost $15,600 per proteome was probably mediocre at arithmetic). 

Whether it was informatics that needed to advance or study design, combining plexes is now common. There are absolutely clearly pitfalls when you do this, but if you've never set one up before this is THE paper you should read first. 

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