I had a couple of Zoomie Team things this week where the conversations landed on MSFragger. Part of that is due to the fact that it is currently the only free way to process a big TIMMYTOF file in reasonable time. (As an aside we had OmicsPCs build us a new box with a water cooled Ryzen 5950X for this purpose. When we ordered it in December I think it was the fastest desktop CPU in the world. Probably isn't now, but we're getting MSFragger searches completed in about 1/3 the time this paper described.)
If you're using FragPipe much, you're probably familiar with this box.
And if you get distracted because, for example, you have an abnormally large 10 week old human who just discovered he has hands and his favorite thing to do when you look away for 10 seconds is punch himself in his own eyeballs, you might forget which peptide.tsv you have open. In this example you should close them all and go try and show him the dozens of frogs that just came out of hibernation that are having a loud jumping and splashing party. Oh. Punching yourself in the face is more interesting than frogs climbing up an 8 foot rock wall just to jump off into a little pond? Cool.
Okay, but the real challenge people point out is that it can be a little challenging to get from your protein to the peptide and PSM level evidence with all the sheets FragPipe generates.
Would a single output sheet like this help?
....and your open search reports all hyperlinked together and sorted out with premade filters?
There are some steps to this, but nothing that will cost you any money and you won't get all the superpowers that FragPipe has, but if you're just searching DDA data with MSFragger in Open or Closed search you probably won't notice (if you've got something other than .RAW you'll need to convert it to a universal format first.)
You'll need PD or a PD demo version.
And you'll need MS2Go (it says it only works in versions up to PD 2.3, but it totally works in 2.4, so I assume 2.5 will be just fine as well.)
I made a tutorial for installing MSFragger in PD a while back you can find that here and I think I put in links to better instructions from their lab somewhere there as well.
MS2Go is super simple. Just point it at your .pdresult file.
And export your condensed report. If you didn't use Feature based quan you'll see this warning that it couldn't find it.
Obviously, this isn't a solution for everyone or every project, but if you or people you work with are used to seeing this kind of a condensed output it will save you a ton of time over assembling this from the FragPipe output yourself!