If your Skyline document has a spectral library in it, you can go to:
Settings > Transition Settings > Library
and change the number for "Pick X product ions".
If your Skyline document does not have a spectral library, you can create one using the menu item:
File > Export > Spectral Library
this will create a .blib file where the "spectra" consist of the m/z's of the transitions in your Skyline document, and the intensities are the integrated peak areas of your chromatograms.
After you have created a spectral library from your chromatogram data, you can go to:
Settings > Peptide Settings > Library
and push the "Edit List" button, followed by "Add", and then point Skyline at your new .blib file.
And then make sure that your new library is checked in the Peptide Settings Libraries checked list box.
After you have done all that, you can go to:
Settings > Transition Settings > Library and change the number for "Pick X product ions".
Skyline will then choose the X product ions that have the highest intensities in the spectral library.
(I would have thought that there was an easier way to chose the top X transitions without having to export a spectral library, but I cannot find it if it exists)
Note that for each precursor in your document, Skyline remembers whether you have manually changed the set of transitions that the precursor has. You can see in the Document Grid which precursors still have their transitions settings managed by Skyline. The column which controls that is "Auto Select Transitions".
If you want to tell Skyline to automatically manage the transitions for all of the precursors in the document, you can go to:
Refine > Advanced
and check the checkbox for "Auto-select all Transitions".
-- Nick |