As of Skyline version 23.1 you can tell Skyline that the chromatograms for a particular precursor should be extracted from a subset of the available spectra.

You can right-click on something in the Targets tree and choose "Edit Spectrum Filter..." to bring up the "Edit Spectrum Filter" dialog.

The Edit Spectrum Filter dialog can be brought up when multiple items are selected in the Targets tree.

If all of the selected items in the Targets tree already have exactly the same Spectrum Filter on them, then the Edit Spectrum Filter will enable editing those filters, and the "Create Copy" checkbox can be used to control whether the current filter will be changed (unchecked) or something new will be added with the new set of filter clauses.

If the selected items have different filters on them, then the Edit Spectrum Filter will be shown with no clauses in it, and the "Create copy" checkbox will be checked and disabled since the only option will be to add new things with the new set of filter clauses.

New in Skyline 25.1

Skyline version 25.1 will allow you to specify a filter that is applied to everything in the document. On the "Instrument" tab in the Transition Settings, click the "Edit" button next to "Advanced Filtering".

This feature can be used to tell Skyline to ignore all spectra matching a particular criteria, such as MS2 spectra with wider isolation windows that were only acquired for the purpose of retention time alignment and which should not be used for chromatogram extraction.