FragPipe team has requested support for defining peptide modifications in Skyline through the command-line. Seems like an obvious next addition to your command-line settings support which initially focused almost entirely on transition settings.

Brendan, the "import-search-add-mods" option tells Skyline to accept all mods from the search. Is this issue referring to only accepting the specified mods, or is it referring to adding/removing mods from the document settings?

This is more fine-grained direct adding of modifications, 1-by-1, definitely should make it possible to add by Unimod ID or SCIEX short-name, and of course the full Matrix Science long name we use... and also giving the full definition of a modification.

This will give users more control of what gets added to the document rather than just accepting everything we guess from the search results. Our guesses are not always 100% correct and a user may only care about certain modifications from the search.

Wasn't intending to resolve it.