Automatic Precursor Isotopes


Skyline can automatically add [M+1], [M+2], etc isotopes to your Targets tree if you provide molecular formulas in your transition lists. Here are some things to know about that.

When you first import a transition list, Skyline will only show the most abundant isotope for precursors in the Targets window.

If you want to see others, there are a few settings that need to be adjusted in Transition Settings (via the Skyline Settings > Transition Settings... menu):

  • In the Filter tab, make sure the Ion types field includes the letter 'p' to indicate that you want to work with precursors.
  • In the Instrument tab, make sure the Min m/z and Max m/z values are suitable for the precursor m/z values you are interested in.
  • In the Full Scan tab, make sure the Isotope Peaks value is set to something other than None.

Note: in Skyline versions 21.2 and earlier, even if you have these values preserved in your settings from a previous run you may have to visit the Transition Settings and make a slight change to your settings to provoke the creation of the additional precursor nodes in the Targets window. It doesn't matter which setting, and you can change it back again afterward, but this is necessary to reevaluate the contents of the Targets tree.

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