Hi Cristina,
Unfortunately, the use case you highlight, adding a single peptide is, as you note, not currently well supported in Skyline. Perhaps, because of its origins as a tool for SRM, Skyline requires you to decide your target peptides before you start importing data, or in the case of SRM, before you even acquire your data.

If you change your mind, and add peptides, then you must re-import your data, which you can do through the Edit > Manage Results form. Just select the replicates you want to re-import, click the "Re-import" button, and then click OK.

This will definitely take longer that a tool specifically built to support adding small sets of chromatograms, usually specifically for a single instrument vendor. Hopefully, Skyline's many other features make up for this less then optimal treatment of adding small numbers of peptides to a document with already imported data.

As for a peptide N-terminal modification, just leave the amino acid field blank, and set the terminus field to N. Another case where Skyline accepts a blank amino acid field is for 15N or 13C labeling of every amino acid residue in the Isotope labeling modifications.

Hope that helps. Thanks for using Skyline.

--Brendan