Are you using a triple quadrupole mass spectrometer (i.e. SRM) or a full scan mass spectrometer?
If you are using a full scan mass spectrometer, you can tell Skyline how many precursor isotopes you are interested in by changing the settings at:
Settings > Transition Settings > Full Scan > MS1 filtering
If you are doing an SRM experiment, or if you are trying to monitor different isotopes from MS2 scans, I do not think there is a straightforward way to do this. You might need to tell Skyline that your peptide is a small molecule and explicitly tell Skyline the precursor and product m/z's that you want to target.
There might also be some way to do it if you told Skyline that your peptide had a modification on it which added some number of Daltons to its mass.