Skyline allows you to specify whether the neutral loss should be included by default.
If you edit the neutral loss definition, there are three options for "Include loss by default": "Never", "Matching Library", and "Always".
If you set that to "Always", then Skyline will give you variants of your ions that include the neutral loss.
You can also add particular transitions to your precursors. You can right-click on the precursor in the Targets tree and choose "Pick Children". If the ion that you want does not appear in the child picker window that pops up, you can press the filter button to remove the filter.
If you don't see the transition that you want in the child picker, you should make sure that "Max Neutral Losses" is at least 1. That setting is at:
Settings > Peptide Settings > Modifications
-- Nick |