We started watching the Netflix show "Narcos" this weekend. We didn't get through the first episode because, well, it was a little too violent for us -- and both televised dog barking and gunshots set our ypuppies into complete chaos.
There is a really interesting description in the opening monolog regarding mice choosing cocaine over food and water. I don't know if that is true, but it makes for an interesting segway into a lot of murder for the TV show. Quiet lab ---> crazy violence.
I haven't been quiet regarding my love of the IonStar methodology developed by the Qu lab in Buffalo and I'm excited to see papers using this technique appearing in the literature!
The gist of the method is this -- if your chromatography is reproducible (even your nano chromatography) you do single shot LC-MS/MS and extract the isotopic profiles from run to run with tight window tolerances and exceptionally tight MS1 mass tolerances and you don't have to fragment every peptide in every single run. This isn't a new concept -- MaxQuant, OpenMS, and soon Proteome Discoverer can all do this. The difference with IonStar is that it is a packaged workflow (and the algorithms for peak detection/alignment honestly do work a bit better than some other algorithms).
You don't get the depth that 2D-LC-MS/MS will give you, but you get pretty darned deep and the more samples you are studying the better -- you just need to fragment that ion one time in the 20 or 50 patient samples to ID it and quantify it across all runs.
Since ASMS 2016, the Qu lab has published at least 4 studies displaying the efficacy of IonStar. And this is where I get back to what I was talking about!
In this one...
..these researchers show the depth that you can get with IonStar in a super tiny amount of sample on an LTQ-Orbitrap system. Excision of the striatal region rats (this is a small internal region of the brain that, I promise you, sucks to get remove even if it isn't THE smallest part of the brain) from rats going through cocaine withdrawal and quantification with IonStar pulls out over 2k unique proteins ID'ed in all runs...and a subset that change markedly in both groups!
Do you have a reference for the original IonStar paper? What about a download? I couldn't find anything obvious on Qu's website.
ReplyDeleteAdam, sorry the IonStar paper is currently in review. Should be out soon.
DeleteHi! First I would like to say since I discovered your blog I have become addicted to it. Starting as a strictly MaxQuant proteomics person, it is helping me a lot to transition into the wider field. Thanks for reviewing all of these cool methods!
ReplyDeleteIn this post, you mention that a peptide identity propagation method is available for OpenMS. I actually am not yet aware of such a node, could you tell me which one does this? Thanks in advance, and keep on with the good stuff!