The way to tell Skyline how many isotope peaks should be included in the Targets tree is with the "Isotope Peaks Included" setting at:
Settings > Transition Settings > Full Scan
You can also right-click on the Precursor in the Targets tree and choose "Pick Children" and unselect the filter button and choose the rest of the isotopes.
The highest isotope m/z that you can add is the monoisotopic mass plus 9 Daltons. Also, any isotope m/z must have a predicted abundance which is at least 1% of the most abundant isotope m/z.
By the way, regardless of the "Isotope Peaks Included" setting at "Settings > Transition Settings > Full Scan", Skyline always extracts chromatograms for all of the precursors isotopes whose predicted abundance is at least 1% the abundance of the most abundant m/z, so, as soon as you add these precursor isotope transitions to the Targets tree you will see chromatograms for them.
-- Nick |