I've been using MSFragger as a standard part of my workflows in Proteome Discoverer for the last 2 years, primarily for rapidly hunting PTMs and for open searching with visualization of the PSMs.
I originally posted this in 2020 and I thought I'd do some updates today, but it's all about the same. MSFragger works just fine in everything up to PD 2.5 and I'm about 11% sure I could just drop the .dlls into the 3.0 and it would work fine, but I haven't done that test yet.
I'm on my desktop in my home office and I've got a PD 2.4 viewer that I use for MSAmanda and MSFragger searches. I do my LFQ quan with
PeakJuggler ap.Quant and that feeds into LIMMA. Most of my workflows on my commercial license in the lab will look something like this (example for TMT quan shown below) if I'm looking for PTMs. I really like having the ability to rapidly screen PTMs by ones identified by more than one search engine before I start flipping through the PSMs manually. I also have some other really cool nodes and you can find notes on those over there somewhere -->
OH. This reminds me about something I should talk about later! I'm actually using a prescreening my spectra up front these days to remove peptides from collagen first. It is crazy how many of our really intense unmatched spectra are collagen with 4 oxidations on them or something. There is some guy in the field who has been going on about this for years and everyone ignores him 😅. We shouldn't be. I'll come back to that at a later date. It just took me a while to figure out how to work filters into my workflows. I actually had to see how Dr. Amol Prakash was doing prefiltering and then that inspired me to make a workflow!
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