Can you send us a .sky.zip file?
In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral libraries and background proteome.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
Can you tell us a little bit more about what went wrong? It sounds like you did:
File > Export > Transition List
and the file you got was not what it was supposed to be.
Can you send us a screenshot of your Export Transition List dialog so that we can see which settings you used? Also, it might be helpful if you could give us the transition list file that you did export.