If you want to download a filtered list of proteomes you only need to select proteomes of interest by selecting the criteria for proteomes and hit the download button.
In the proteomes view expand the gray box "Advanced search". Here you can select the domain of life that is of interest to you; select desired PQI score; user score; and source of proteome. Alternatively you can type in a string (word or a part of) in the white search box at the top of the page that returns all proteomes whose names match the input string.
You can search proteomes by common name (for example "Western Gorilla") or taxonomic classification (for example "chordata")
All proteomes visible in the view, and those listed on subsequent pages are "selected" for download. Please make sure you constrain your selection criteria enough to download only your desired proteomes.
A download will initialize shortly. You will recieve a zip archive containing fasta files for all selected proteomes.