Mike found that the speclib's TSV version (not the report TSV) has an ExcludeFromAssay column. Can we use that to pick only transitions that should be used for quantitation in Skyline (e.g. they aren't present in only a small number of runs)? Is that column available in the binary speclib (up to now we've only needed to read the report TSV and the .speclib file)? I've asked Vadim and will update with his answer.

To use this column, BlibBuild will need to use RefSpectraPeakAnnotations to annotate either excluded or included peaks. To keep the blib and read time smaller we'd probably want to make the default state (unannotated) be the most abundant one. Looks like the most abundant is False:
False    True
78992    33283

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.