So many ways to process DIA data! Which one is best? This new preprint tries to answer the question that we've also been working on recently at Hopkins!
DIA-Umpire has been integrated into FragPipe. If you've got an older instance of DIA-Umpire, I strongly suggest you try the updated FragPipe. It's a lot easier to use this way.
We're demo'ing SpectroNaut now and I really like it. At $6k/year for an academic license (my understanding is that it costs more for cores) it ain't cheap, but it's by far the most intuitive to set up processing. The data interpretation....is...well...interesting. It's really pretty with all these QC graphs and things up front, but finding something like "these are my replicates and this is their relative ratios" requires more digging than you'd guess.
DIA-NN is crazy powerful, but the data comes out in such an odd and sideways way that your job isn't done when the software is. There is an R package for working with the data, though. DIA-NN will also build your libraries directly from FASTA like DIA-Umpire/Fragpipe and SpectroNaut.
Skyline is, of course, Skyline. If you know how to use is, it's probably the best thing out there. If you don't know how to use it, it seems like a confusing maze of "where is anything". As it adds power and hides more features in places that might make sense to people using it for the last 10 years, it is becoming my least favorite software to show to students unless we can get them off to a workshop immediately. Like MaxQuant I don't know how this is avoidable, so this isn't really a criticism, but I think we're all accepting that you can't really master these software packages unless you fly to a workshop.
I haven't tried OpenSwath in years and I'm sure it's come a long way, so that should be on the list for me to give a whirl. At a shortish stop on my career recently we had ScaffoldDIA and I think that if you like Scaffold, you probably want to get a demo of that one.
Pinnacle didn't make this list. I'm a big fan, but I'm extremely biased, because my friend and long time coworker wrote it. It ain't free either, but since you buy what modules in Pinnacle that you want (or pay an annual fee for them) it can be an affordable solution for specific applications. This year I needed small molecule targeted, metabolomics, proteomics, and large molecule and I think that set someone back $6k for my annual licenses. I'll probably only go for proteomics module next year. Out of what I've tried, Pinnacle has the most intuitive visualizations, particularly if you've got a big ass monitor. (Is anyone else using TVs instead of monitors? $200 for a 27 inch monitor? Or $150 for a 47 inch TV? I'll never buy a monitor again! You get thumbnails for your DIA transitions for each peptide on your main screen so you know up front if you've got a lousy hit for something you're interested in. You can also get a permanent license, but it's made sense for me to shuffle my licenses due to different projects.
There are more DIA options out there, and more coming all the time. I'm glad these authors did a thorough pressure test of multiple datasets and you should 100% check it out!
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