Proteome Discoverer 2.5 just launched this week. You can get it from the ThermoFlexeraFlexibleNet thing here. I think there was a lot about it at the fall user group thing, but I still haven't caught up on all the talks from ASMS that are on my list, the single cell proteomics thing at NorthEastern, and HUPO was last week.
If you're going to use it please keep in mind that it will default to 1 processing and 1 consensus workflows. If you queue up 60 things on your 72 thread PC and go out for a bit, you might be mad when you get back. Install it, go to Administration, parallel workflow settings, set it to something reasonable, then close and reopen the software.
I just downloaded it and am messing around and it looks a lot like version 2.4 with one big new focus:
You can basically run what I think from the manual is basically PROSIT, directly in Proteome Discoverer!
You go to the Maintain Spectrum Libraries thing that has always been there that you've justificably never used:
What do you do with your fancy new library? You can use that to search things instead of dumb ol' SeQuest because now you're fancy new library can go right into an improved MSPepSearch that can run multithreads!