I feel like this paper, though still in PrePrint only, might have made this blog once before.
Much better! (Most colorful thing I could think of in 2 seconds).
Back to the paper! Here is the idea -- fine -- do your normal peptide search with your full database -- but do your FDR decoy search against just the peptides you identified.
Which -- you know -- kinda makes sense, right? If your database is way bigger than your matches (which is true in everything I can think of right now) then you have a much higher chance of false matches if you reverse it. But...I have no way of testing whether this idea is smart or not.
Oh wait -- they set up a webpage where you can test this premise on your own data just to show that they're onto something!
Here it is!
You'll need to get your PSMs into the format they they want (CSV, with specific comma placements) but the output charts will show you your results if you do normal target/decoy vs. their hybrid approach.