Are you asking what sort of data Skyline might send to other servers?

Skyline uses a service called "Koina" to do peptide spectrum and retention time prediction.
The Koina feature is turned off by default but if you go to "Tools > Options > Koina" and make some selections there then your peptide sequences will be sent to the Koina service.

The other thing that Skyline does is request protein metadata (gene, species, etc.) from the uniprot web server. Skyline sends your protein names and descriptions to the uniprot web server. There is currently no way to turn this feature of Skyline off, but we could potentially add a way if that was important to you.

These are the only things that I can think of where Skyline might send data to another server in the background without you telling Skyline to.
-- Nick

Hi Nick,

Thanks for the quick response!

When you say that Skyline sends the protein names and descriptions to the Uniprot server, do you mean that it would be sending sequences to the server? I think this might be an issue for us, but I will double check with my supervisors.

I know we're missing out on a great deal of Skyline's functionality here, but I was really just hoping to be able to generate a list of theoretical peptides, their intact masses, m/z's, and transitions using our sequences. If I were to copy and paste the sequence into a blank document instead of ever saving or importing a FASTA, would that prevent things from being shared to an external server? Additionally, could the software be run without internet connectivity?

Thanks again for your help!

Seamus