Hi Joe,
Absolutely. You need to add the modification "Water Loss (D, E, S, T)" to your document. Once you do this, all peptides with D, E, S, and T will allow the appropriate loss in their fragment ions. If you use a spectral library, Skyline will pick these ions from the library spectrum when they are the most intense. Otherwise, by default, you would need to pick the loss transitions manually.
If you need more detailed steps for how to achieve this, just ask and I can give them. If you already feel comfortable working with peptide modifications in Skyline, then this may be all you need.
--Brendan