Dan Polansky pointed out that importing a transition list with a lot of potential modifications can get very slow. This is because we try all of the modified states for rows with a bare peptide sequence. We need to detect when we truly have a column where we expect a modified sequence and when we are allowing a bare sequence, and only try all modifications when we truly only know the bare sequence.

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