Wael,

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 extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request.

Otherwise, you can upload it here:
https://skyline.ms/files.url

-- Nick

Hi Nick,
due to some confidential issues, I am afraid that I am not allowed to share the lib. besids it is 3 GB after creating the .zip file.
sorry for that.
Best
Wael

In Skyline, when you do:
File > Export > Spectral Library
Skyline creates fake spectra whose intensities are equal to the integrated peak areas of your MS2 chromatograms.

One reason that you might end up with an empty spectral library is that you really do not have any MS2 chromatograms in your Skyline document.

It might be that you do not want to export a spectral library, but you actually want to build a spectral library from your peptide search results.

In Skyline, when you do:
File > Import > Peptide Search
Skyline creates a spectral library for you. Skyline names the spectral library the same as your Skyline document, but gives it the extension ".blib".

Another way to build spectral libraries is:
Settings > Peptide Settings > Library > Build

Can you give us more details about what you are trying to do?
-- Nick

Hi Nick,
thanks for the feedback.
I basically used the first option to create a lib (File > Import > Peptide Search).
I want to create a spec lib. from fractionated samples (total 115 raw files) --> export the lib from skyline--> and import it in ProgenesisQI --> and let Progenesis search for peptide identification in the actual samples and continue with the LF quantification.

I will try the second option you mentioned (Settings > Peptide Settings > Library > Build)

Thanks
Wael