Yesterday I was visiting some of my favorite labs and got a great question from a great scientist! If you are in one study in Proteome Discoverer, it is very easy to combine previously processed datasets. You just highlight the ones you want and Reprocess. If 2 files are selected, the ability shown above to "Use Results to Create New (Multi) Consensus" reports appear.
The question was: How do you combine results from different studies. When I was actually in the lab, I made this too complicated. I just discovered it is very easy.
Just add the .MSF files you want to combine into the same study.
Add the .MSF file the same way you would add a new .RAW file and PD adds it right into the Analysis Results tab. Then you can make a multiconsensus report.
I accidentally tested files from different hard drives. Totally works! Though, it didn't finish the consensus until I was almost done typing this, so it might have taken longer than normal...it is too nice outside to investigate!