Clear up the confusion and regenerate your productivity with FragPipe DIA!

 

A very common conversation I've had the last year is about the DIA-NN + FragPipe paper and how no one has been able to run DIA-NN successfully through FragPipe.

(this one) 

Around version 17 (I forget) a new DIA-NN tab appeared in support of that preprint and that sounded great, everyone tried it and no one could get it to work.

I even went to the amazing (how they possibly support it at that level) FragPipe Github support and asked the question and cleared it up for myself. 

And the confusion can be cleared up by this statement: 

You can't actually run DIA-NN through Fragpipe. You can quantify things using DIA-NN in FragPipe, but you can't identify things with DIA-NN in FragPipe. 

If you want to identify things AND quantify them, you need to use DIA-NN. Don't use Fragpipe.

Got it? Me too! It just took me a while! 

Let's clear up the confusion ever further! Forget DIA-NN entirely! Run MSFragger-DIA through MSFragger! 

What's Vadim doing on this paper? I dunno. I think we're all just supposed to put his name on everything now if you want a paper in a Nature family journal. Or he's collaborating with just about everyone. One of those things. (Edit. I'd just like to clarify that this is a joke, I think we're all floored by the output of this young researcher and the quality of work that he's consistently putting out there in the world.)

Why would you switch it up if you're already using DIA-NN? 

YOU CAN REGENERATE YOUR CAREER WITH TIME SAVINGS! Hard to tell from the scale, but is that 1,000x faster? 

And check out the UpSetR on the very top of the post in Figure A. The same results in 1% of the time?