The following support request has a description of how the fold changes are calculated:
I am not sure I understand your other question. It sounds like you are saying that you imported DIA-NN peptide search results and the number of proteins in your Skyline document is not as much as DIA-NN says that you should have.
I would recommend that you first ignore the number of proteins that you have and instead only focus on the number of peptides that you have. Once you have all of the right peptides in your document you can use the menu item "Refine > Associate Proteins" to move those peptides around to different proteins and your choices about FASTA file and protein grouping will affect how many proteins you end up with. (In order to figure out how many peptides are in your Skyline document you should first use the menu item "Refine > Remove repeated peptides" and then look at the number of peptides displayed either in the status bar at the bottom of the Skyline window or by looking at the number of rows in the Document Grid when you are looking at the "Peptides" report).
One way to be more certain that you get all of the peptides from your search results into Skyline is to use the menu item:
View > Spectral Libraries
and then press the "Add All" button.
If you leave the "Associate proteins" button unchecked when you press the "Add All" button, then all of the peptides which had been missing from your document will get added to a Peptide List called "Library Peptides" and you can look at those peptides and figure out why they were not included in your original set of peptides that you got when you imported your peptide search results. The most common reasons have to do with the settings on the "Digestion", "Filter", "Library" and "Modifications" tabs of the "Settings > Peptide Settings" dialog, and the "Filter", "Library", "Instrument" and "Full Scan" tabs of the "Settings > Transition Settings" dialog.
You certainly can send us your data files and we can figure out what is going wrong. We usually learn a lot whenever we look at large datasets like this, and we are in the early stages of creating a process by which you will be able to create a Skyline document which has all of peptides from your DIA-NN search results.
I will send you an email.