|Title||»||Import > Assay Library should automatically recognize Water and Ammonia losses|
Import > Assay Library currently automatically recognizes peptide sequences with modifications specified and automatically adds appropriate modifications to the document, but it still requires the user to manually specify water and ammonia losses, and even if they do add the Skyline default "Ammonia Loss (K, N, Q, R)" and "Water (D, E, S, T)" modifications, one of the more popular sources (Biognosys Spectronaut) of this tabular format library type allows ammonia and water losses on any fragment ion.
What we should try to do is automatically detect when loss ions are being specified and when they are being specified on fragments out side the AA residue boundaries that our default modification types allow. When they are specified inside our allowed boundaries, we should just add our default modifications automatically to make the import work, when they are allowed more liberally, Skyline should warn the user that the assay library appears to contain losses not supported by our defaults and ask whether Skyline should: 1) use the defaul loss modifications, 2) use ammonia and water loss modifications which allow these losses on any fragment ion.
I have a couple of good examples of this type of library generated by researchers using Spectronaut. These files also contain a column "FragmentLossType" (noloss, H2O, NH3) which would be good to recognize and then only match fragment ions with the appropriate loss type, i.e. a transition with H2O should not be allowed to match an ion without that loss.