Tuesday, May 19, 2020

Offset multiplexed targeting -- The brilliant targeted method you should have thought of first!

I have been dying to talk about this paper and it is finally out!

If you have been running a mass spectrometer of any kind -- get ready to feel reeeeeeaaaaaallly dumb that you didn't think of this first.

I'm allowed to say that I was lucky enough to be one of the reviewers if this, right? And this extra time has been very useful becaus my ego has almost recovered from never once thinking of this myself.

If your name isn't on that list of authors above, I'm going to now refer to you (and myself, of course, because I'm just as guilty as you are) affectionately as...I dunno...let's go with "Dumbass"

Hey Dumbass! You know how you can get a heavy labeled peptide for anything you want? Heck, you can even order complete heavy labeled peptide mixtures?

Oh -- you knew that? Good. So did I.

Hey Dumbass! Did you know that you can offset your fragmentation window?

Oh -- you knew that too? Yeah. So did I.

So....Dumbass....did you ever put these things together and think -- I could just put in my heavy labeled peptides and when those triggered, just offset my fragmentation backward to where the light peptides would be?

No? Neither did I.

I can't overemphasize how much I am going to use this technique. You can essentially bypass all the challenges of PRM with the addition of a heavy peptide standard that you target and then offset.

You need to do a little bit of math to work out your offset, if -- for example -- I just wanted to characterize a pathway of interest, all you need to do is get heavy peptide standards for that whole pathway. They make kits for these.

There are complete whole protein and phosphoprotein heavy peptide standards for entire pathways....

...as well as for critically important central proteins like TP53 which are almost impossible to monitor with traditional proteomics due to their exceptionally low expression levels! 

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