However, Skyline has extremely flexible custom annotations that can be assigned to any of 7 levels:
- Proteins
- Peptides
- Precursors
- Transitions
- Replicates
- Precursor Results (essentially an integrated group of transition chromatogram peaks)
- Transition Results (essentially an individual integrated transition chromatogram peak)
So, if you want to categorize your proteins by function, you would want to define an annotation (using Settings > Document Settings - Annotations tab) on Proteins and then fill in the category for each protein. This will allow you to export reports with the annotation associated with each protein, and it would allow you to use the Skyline Document Grid pivot editor to calculate some summary values by these categories directly in Skyline. See the PowerPoint slides on the pivot editor on this page:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=new-4-1-features
If you had clear ideas on features you hoped Skyline might have around protein function, though, please do share them with us, as Brian suggests. We are always interested in hearing user feedback.
--Brendan