I've got a pile of huge O-link population level proteomics studies on my desktop to rant about at some point. However, at some point a blog post has consumed so much of my time that I think "maybe I should float this by an editor to see if I can get real world credit for those hours" and I made that mistake yet again with that one.
I love proteomic discovery work. I don't think we've found anywhere near all the protein post-translational modifications that matter in humans, and that's how we'll find them. Heck, we don't even know how many f'ing proteins there even are. The biologists, however, don't seem to have the patience for these primary discoveries. They want large n targeted studies and they want them yesterday.
You can PRM a decent number of targets at high resolution. A stellar student in my group did 300 targets on a ZenoTOF but that's WAY more than I've personally set up. I don't know if I've done more than 40 on a Q-Orbitrap ever.
Sure QQQs are fast, but in real biological matrices for MRM/SRMs? You need a crapload of transitions and you need a synthetic peptide for every one. There's just too much noise.
An O-link bigtime assay (maybe that's what they call it? something like that) that uses a super high throughput (and increasingly unreliable - some of that new Illumina super multiplex stuff has a load of garbage artifacts in it) can target (and, please remember, target doesn't necessarily mean detect) thousands, and that really hasn't been in reach for LCMS
Until now? Can the handy dandy super fast little unit resolution ion trap target on that same scale? These people seem to think so.
At first this doesn't seem all that impressive, right? I did nearly all of my PhD work on the new-at-the-time 3200 QQQTrap system. Triple quad with signal boosting trap on the end. Yawn. Same stuff.
My QQQTrap couldn't do >100 scans/second. And it sure as heck wasn't more sensitive than any QQQ on the market today. The trick, though, is in the combination of really sophisticated control software in combination with quantitative software everyone in the field except for me is really good at using.
The authors take the Biognosys 600-ish targets for plasma reagent kit and demonstrate really good quan even when running 100 samples/day. What's that? 14 minutes run to run? Something like that. But with the number of concurrent targets that can be measured per cycle, it's clear they could add on a crapload more and have the cycle time to pull them off. It'll probably be a question for the community soon, for how many points of confidence do we need for unit resolution PRMs? Given the full blown acceptance of tools that predict peptide fragmentation patterns, retention times and ion mobility when available in wide window experiments....I dunno, it's hard to see too many problems with targeted quan without a heavy internal standard for every peptide. I'd betcha two of my kid's newly acquired KitKat bars that the quan is better than the O-linky and Aptamer-ma-bobs.
No comments:
Post a Comment