Alright, this DIA stuff is confusing. There are methods all over the place. WiSIMDIA on the Fusion, pSMART, multiplex-DIA, and even boring old SWATH. Software-wise, there is tons of stuff out there. This weekend I processed some DIA data from a Fusion directly through Proteome Discoverer 2.0...and it looks amazing.
The data in question was ran through the DIA-Umpire to convert the data into a handy-dandy MGF file format. You can find details on the DIA-Umpire in this Nature Methods paper by Chih-Chiang Tsou et al., out of Alexey Nezvizhskii's lab. Essentially, it is a (currently) command line driven program that takes your DIA data and "deconvolutes" it down to a format that is friendly to the proteomics processing pipelines we already know and trust. How does it work? No idea. But it works, and the data looks amazing (did I say that once already?)
Here is a random high scoring PSM I grabbed. Looks pretty incredible, right? They all do. And I didn't have to change my workflow at all. I used SequestHT, target decoy and my normal basic consensus report. I ended up with a ton of IDs and really nice true FDRs at every level I set them at (PSM, peptide, and protein).
If you are interested in identifying peptides via DIA and you are a little swamped by your software options, you might want to check this out. I'm tired of learning new software interfaces -- lets put everything in Discoverer!
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