Starting in Proteome Discoverer 2.0, we now have the ability to directly download FASTA databases from ProteinCenter. However, it might look a little confusing if you select that option from your FASTA file menu in Administration.
What you need is your Taxonomy ID. For example, if you want to autodownload all the SwisProt entries that ProteinCenter has for our species you'd want to use code 9606 and click the Import button.
How do I find these Tax IDs? I use this thing!
This is the NCBI Taxonomy Browser (click here for direct link!). Just put your species name in the top and it'll come back with your organism and the Tax ID at the top.
There are several other such tools available on the web, but this is a quick and easy one.
Important note if you use this tool: Once you download a FASTA from ProteinCenter, you now have the ability to search for updates when ProteinCenter posts them. If it finds one it will directly copy over the FASTA you have in place. If you are in a role where you need to keep a constant record of where you obtained your FASTA and when, it might be easier to download them yourself the old fashioned way so you can keep a time stamp and record of each individual FASTA.
Shoutout to Brad for pointing out that this process could use some clarification!