Wednesday, March 14, 2018

Benchmarking quantitative strategies for phosphoproteomics!

Shoutout to @PreOmics for tipping me off to this one (great job Google Scholar alerts -- how'd you miss this one?!?)

I can't even get through this one this morning -- daylight savings time is dumb, but considering we're about to fire up a 10 time point 3 replicate per time point phosphoproteomics study on something that sounds super important (I forget what) it couldn't have shown up at a better time!

At 30 samples we're just at the critical junction where TMT 11-plex should be perfect for it. We'll probably miss some channels moving from plex to plex, but we'll save so much time that it has to be worth it (and that 11th channel is our great pooled control!). The next decision -- it's phospho -- do we break out the MS3 SPS to deal with our ratio compression, knowing full well that the lower speed of the method is going to mean fewer total phosphopeptides?

THIS TEAM GOES THROUGH ALL OF IT!!!  THEY EVEN SPECIFICALLY LOOK AT DNA DAMAGE PROTEINS (which may actually be something like what we're doing -- but...again... I can't remember. You know, it's actually better science, I think. All of my experiments are double blinded. I can't interject unintended bias when I can't remember what organism or project I'm working on!)

Speaking of biases -- this study does a pretty nice job of supporting one of mine. TMT MS2 methods look pretty impressive compared to MS3....definitely check it out!

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