I modified my own copy of BiblioSpec so that it would include all of the peptide spectrum matches from the Mascot DAT file.
I uploaded the .blib file that I made here:
I am not sure whether this .blib file would be useful to you.
In your .pdf file, it looks like it is saying that YNHINAK got a score of 14.4, which is better than
YSPTSPK which got a score of 13.0
One thing that you can use this "full_filtered.blib" file for is to see which ions in the spectrum Skyline thinks match up with the theoretical ions from the peptide. With the default settings (0.5 m/z tolerance, and only showing b and y ions), only two ions from the observed spectrum match theoretical ions from your peptide (see "YSPTSPK_default.png").
In Skyline, you can adjust the tolerance with which Skyline matches theoretical ions to ions in a spectrum, using the "m/z match tolerance" setting at "Settings > Transition Settings > Library".
If you do that, and you turn on "A" ions, you get the picture I have attached "YSPTSPK_A_Ions_1mzTol.png"
My understanding is that your mass spectrometer (orbitrap?) is unlikely to produce A ions, and also should have a mass accuracy which is much better than 1 unit.
I am pretty sure that YSPTSPK is not the correct match for this spectrum.
Let us know if you think Skyline is doing something wrong with the way it is interpreting these Mascot search results.
Is there a reason that it is important to you that this peptide be in your spectral library.
You can always add peptides to your Skyline document using the menu item:
Edit > Insert > Peptides
You can specify the modified sequence of the peptide in the Insert Peptides dialog as:
(You can also right-click on a modified peptide in the Targets tree and choose "Modify" to apply modifications to it).
One thing that spectral libraries are helpful for in Skyline is for choosing which transitions to monitor. However, in this case, you would probably do better choosing the transitions yourself. You can choose precursors and transitions by right-clicking on things in the Targets tree and choosing "Pick Children".
Hope this helps.