Halloween TMT CageMatch -- MSFragger vs Proteome Discoverer +Chymerys!

 

FragPipe can do TMT stuff (as long as you aren't using a TIMSTOF or ZenoTOF) and it has totally looked impressive so far. How would it do against Proteome Discoverer with the fancy new Chymerys AI thingamawhatsit? 

Here ya go!

In the end, it looks like both do pretty well in terms of overlap, maybe the quan is a little better with FragPipe and maybe the number of IDs are a little higher with Chymerys. 

What the authors are concerned with is time for big cohort studies and this is where FragPipe really shines. FragPipe is massively faster here. 

Just to be argumentative, I'm still just here running MSFragger inside of Proteome Discoverer and doing my TMT with the IMP nodes so that I can get MSFragger speed (almost) and get all the visualization tools I want (and all of that is free stuff unless you're in a company). I do plan to finally check out Chymerys cloud soon and I got a free demo to check out when I find time.