Congratulations! You're about to submit a manuscript. I, quite seriously, probably can't wait to read it. Shoot me an email if it's really smart. I can't guarantee I'll put it here, but I'm always looking for tips on what to read next.
Okay -- now you've got to get that data uploaded somewhere so the reviewers and nerds with insomnia can download and look at it, right!?!?
If you haven't submitted data in a while and you're using a new version of Proteome Discoverer you might rapidly find that the tools you used to use for PD 1.x require you upload a .MSF file.
Your results in PD 2.0 or newer are actually something called a .PDresult file. (You have an MSF file, but it isn't your FDR filtered results). Don't fret. You can directly export the data out of PD into mzIdentML (which is often shortened to .mzId -- just to keep you on your toes.)
Open this revolutionary dataset that you have generated in PD 2x (2.2SP1 pictured) apply your filters, and export your mzIdentML or mzTab. Boom! Done!
Add that to your complete submission.
Oh -- this is a great recent shortcut as well -- you can, of course, still directly upload to your storage site of choice, but if you are using a ProteomeXchange partner, you can shortcut by using the PX Submission java GUI. You can download it here.
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