I am not sure I understand your question.

If you want to add some peptides to your Skyline document that cannot necessarily be digested from a protein sequence, you can use the menu item:
Edit > Insert > Peptides

If your Peptide has at least one Precursor in it, then you can create a Custom Report in the Document Grid which includes the column "Precursor Neutral Mass".
You can learn about Custom Reports and the Document Grid here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

If your peptide precursor is charge 1, then the difference between the Precursor Neutral Mass and the Precursor Mz will be the mass of a proton. That is, for peptides, the Precursor Neutral Mass is 1.00727649 Daltons less than the charge 1 Precursor Mz.
-- Nick