The output from Proteome Discoverer is an MSF file. The output is trimmed down to be what has been deemed the most useful data for the average PD user. But what if you want more? What if you are curious about your Decoy matches, or just want to dig in deeper in order to develop your own nodes?
Fortunately, Proteome Discoverer keeps all that data in the MSF file, you just need a second program to open it up. At the PD user's meeting, Bernard Delanghe mentioned SQLite as a software to use to get to this extra information.
Now, if you are doing this for fun like me, you can get SQLite home for free. You'll have to pay for it if you are using it for work, but they also have a free demo so you can check it out. You can get it here.
What information does it get you? I think a better question is what do you want!?! Or what don't you want?!? I opened a PD MSF file from a 2 hour HeLa run in SQLite and it gave me 71 data and processing parameter categories in the nice, well organized and easy to read output shown below.
71 categories! I highlighted the decoy peptides, because it is something I was recently asked about. The MSF file has just an unbelievable amount of data in it. And if you use this program or something like it you can get to all of it.
For most people, though, PD has the data up front in the format that you really need. If you want a feature moved to the front in PD for easy access you can always make a request on the BRIMS software portal. A feature that I requested is now present in the alpha version of Proteome Discoverer 2.0. The developers aren't spending the kind of time in labs that we are and feedback is necessary to make the next versions even better.