Can you send us your Skyline document?

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.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

It might also be helpful if you could send us the files that you used to build your library. It sounds like that was a .ssl file and maybe some .ms2 files. If you would like, you could zip those files up and send them to us too.
-- Nick

Thank you for the response, I have uploaded the requested files under 271122_jtsorren

When you build your spectral library, there is a checkbox on the first page "Keep redundant library". You should ensure that that option is checked.

When you tell Skyline to create a library called "test.blib", Skyline always first creates a file called "test.redundant.blib" which contains all of the spectra that it has been told to put in the library.
Then, Skyline runs a program called "BlibFilter.exe" which looks at all of the spectra in "test.redundant.blib" and, for each unique molecule and adduct, decides which is the best spectrum. BlibFilter.exe creates a file called "test.blib" which contains only the best spectra.
After that, if "Keep redundant library" was not checked, Skyline deletes the file "test.redundant.blib".

In the Spectral Library Explorer, Skyline will notice whether "test.redundant.blib" exists, and, if so, will display a dropdown under the spectrum graph which lets you select different spectra from test.redundant.blib.
When you push the "..." button in the Spectral Library Explorer, Skyline tells you how many spectra could be found in "test.blib", but (I believe) does not tell you about the spectra which are in "test.redundant.blib".

-- Nick

Thank you, that was exactly my question.

One additional question, if I want to combine an experimental spectral library built here with a theoretical library build is there a way to combine the uploaded transition list with the targets imported from the Library Molecules?

When using File -> Import -> Transition List... there becomes a new Target list with several overlapping transitions, but several new ones. I would like to have the transitions added to the Library Molecules as some of the new ones are seen in the spectra.

I have attached a theoretical transition list here for your exploration. Thank you!

I think what you would need to do is create a Skyline document with all of the transitions from the library.
Then, export a transition list from Skyline.
In this case, you are going to want to read that transition list back into Skyline later. I am not sure what the best way to export a re-importable transition list is. One thing that you can do is:
File > Export > Report
and export the report called "Small Molecule Transition List". That report might have some extra columns which Skyline will not understand when you try to reimport it, so you might have to use something like Microsoft Excel to remove the columns that you don't want to reimport.

Then you will use Excel to combine the transition list that you just exported with the transition list that you already have.
Then, you import that merged transition list into a blank document, and you will have the custom transitions that you asked for as well as the transitions from the spectral library.

If this does not work, then you can send us your document, spectral library and transition lists and we might be able to come up with another workaround.
-- Nick

Thank you, I will use this methodology to attempt to combine the two libraries.

I noticed that under Settings -> Transition Settings... -> Library I am only allowed to pick 50 product ions maximum. Several of my theoretical peaks are in the spectra but do not get picked. Is there anyway to increase the number of product ions picked in skyline?