A common way to get lists of proteins into Skyline is using the menu item:
File > Import > FASTA
A FASTA file has descriptive lines that start with ">" followed by one or more lines containing the protein sequence.
The first thing on the ">" line is typically a protein accession number. If Skyline is able to understand the format of the accession number (e.g. "sp|Q9D2V8|MFS10_MOUSE"), then Skyline will try to fetch the gene name, etc. from the uniprot website.
Also, there is some way to specify the gene name etc. in the ">" line in the FASTA file, but I am not sure how to do that.
I do not believe there is any way to edit the gene and species. The typical place where you might edit things like that would be the Document Grid, but those columns seem to be read-only in the Document Grid.
If you would like to learn more about the Document Grid you should look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
If you have additional information that you would like to associate with your proteins then you might want to define a "custom annotation" which is talked about in the Custom Reports tutorial on page 28.
-- Nick