I made this statement twice in one week recently "what we'll give you from this experiment is a very large list of phosphopeptides and their relative abundances, and if you figure out what to do with it, please let us know"
BECAUSE I DON'T KNOW WHAT TO DO NEXT.
Sure, I can go to PhosphoSitePlus and I can see that my phosphopeptide has been found before and when (yay....)
Or I could pretend these are genes and put them into IPA and generate...well...something....
As a field, I think we've done a great job of ignoring this. Fixing it? That would be really hard. But -- I think that Perseus is sneaking in a solution.
Check this video out (did I post this before?)
There aren't loads of details on PHOTON outside of the video -- and here is where you can get the software to load into Perseus (188.8.131.52 or newer, though, I think this might be the newest). I presume there is a ground-breaking paper on the way!!