What if you could just about do it for free?!?! What if it just requires switching your solvents around and adding an enzyme to degrade the DNA/RNA? That's what they show you can do here!
Okay -- so they only increase the numbers by like 50%. But that's still a lot!!
What you're doing is just switching up the protocol to drop the amount of crap that is also sticking to your enrichment column.
By UV it looks like this:
A has a lot of crap! B has WAY LESS crap! And that's all there is to it, your instrument spends less time trying to sort out your already-difficult-to-ionize-and-fragment phosphopeptides from a bunch of other stuff and you get more IDs.
As a side effect, maybe missing all that junk is a great way to further preserve column life and keep the instrument cleaner longer.
Even if it doesn't? 50% more phosphopeptides!!!?!?!?!