Thank you for uploading that zip file.
Unfortunately, there are a few files missing such as the spectral library and background proteome files. Also, I see there were some .skyd files in there, but I am not sure whether those .skyd files are the ones that belong to the .sky files.
It would be very helpful if you could use the Skyline menu item "File > Share" to create two .sky.zip files and send me those two .sky.zip files.
When you use the "File > Share" menu item, Skyline puts all of the necessary files into one .sky.zip file. If you try to put the files into a .zip file yourself, you will probably forget to include some necessary files, so it's nearly always best to use the "File > Share" menu item when you want to send a document.
You can upload those .sky.zip files here:
The .skyd file contains the data for the extracted chromatograms. The menu item "Edit > Manage Results > Minimize" is useful if you have deleted a lot of peptides from your document. If you have deleted peptides from your document, the chromatogram data will remain in the .skyd file until you do "Edit > Manage Results > Minimize" or you do "Reimport" or something like that.
The other thing that you can do in the Minimize Results dialog is tell Skyline to discard the parts of the chromatogram which are outside of the chosen peak. That is, if you choose "Limit noise to 1 minutes before and after the chromatogram peak" then Skyline will truncate the chromatogram so that it only extends one minute before and after the selected peak.
If you have not deleted a bunch of things from the document and you do not tell Skyline to truncate the chromatogram, then "Minimize Results" will not have a significant impact on the size of the .skyd file.