There is a column "Library Intensity" which you could see if you create a custom report in the Document Grid.
That is the actual intensity value from the spectrum in the spectral library.
It is not a relative abundance value like you are asking for. If you wanted to get it as a percent you would need to export the report to Excel and then calculate it using a pivot table.

There is also the column "Library Rank" which tells you the transition's position in the list of library transitions from highest intensity to lowest intensity. Most of Skyline's features for choosing transitions from a library revolve around setting the cutoff in terms of how many transitions to choose, which would be the maximum Library Rank. Skyline does not have any features that I know of related to the sort of percent that you are asking for.

Does this answer your question?

By the way, Skyline will show you the intensities from the library spectrum in the "View > Peak Areas > Replicate Comparison" window but not when the graph is showing precursors and products on the same graph.
So, to see the "Library" bar graph you have to do right-click on the graph and choose either "Transitions > Split Graph" or "Transitions > Products". When you do that, you will see a bar graph representing the intensities from the library spectrum and you might be able to visually decide which transitions are below the 5% cutoff that you want.
-- Nick

Hi Nick,
Thanks a lot for your answer and explanation, but my request is not solve.
As discussed with Brendan two week ago during EMBO course in Barcelona could be very helpful for us, and I guess for others, to have a systematically way in skyline to refine library, by number of transition and/or Relative Abundance.
Best regards,
Guadalupe Espadas