Unfortunately, no, after you have added the new peptide, the only way to extract chromatograms for it is to tell Skyline to extract chromatograms for everything else as well.

You can use the "reimport" button at "Edit > Manage Results" to tell Skyline to extract chromatograms again.
--Nick

Do you think this feature of integrating peaks only for new/modified targets (and not for unchanged, previously imported targets) will ever be added? It would be really helpful.

Some additional thoughts/comments about the importing interface/process:

I recently experienced a situation when trying to re-import a large document with 100+ files in order to add a couple new targets, the import stalled for several hours and so I tried to cancel. Unfortunately, starting the re-import appears to have deleted the entire Skyline chromatogram data file, such that even when I closed the Skyline document without saving and reopened the unchanged Skyline document, I still had to re-import all the previously imported data (despite not saving changes/new targets). Is there a reason that the chromatogram data file is deleted immediately at the start of import, instead of perhaps creating a temporary file that replaces the previous version only once the import completes successfully?

Secondly, it would be helpful if there was an intermediate step between selecting the files for import and starting the import. For example, files for a project may be within separate subdirectories (e.g., "Batch1", "Batch2", or separate run dates), but as far as I am aware, one cannot create a "list" of files for import from separate directories. This means that I have to import each set of files from each subdirectory separately, wait for that import to finish, and then start the next one, etc. This means that I have to repeat the process every few hours in order to get the whole experiment imported. Ideally, one would be able to import all the files at once from multiple directories and let it run overnight. I grant that I could move all the files to one directory, but this would be an issue where the file directory structure is mandated (e.g., in a core facility). Alternatively, moving them to a single directory, importing, and then moving them back to the original subdirectories would also create the separate issue that Skyline would not be able to find the files for spectra viewing or other operations.

Finally, there are situations where the file location may have changed (e.g., new data server address or the moving files situation above). Currently, Skyline will return an error that the files cannot be found. When this situation arises when using Proteome Discoverer, there is the capacity to update the file locations without the need for re-importing or re-doing the analyses. Do you think this feature will ever be added? It would be helpful in general but also may be an easier way of addressing the importing headache mentioned above, vs. creating a new interface/workflow for importing files from multiple directories.

Overall, as always, thanks for your continued development of such a great program.

Josh