reopen
From Alexey:
One minor thing is that in the FASTA files import GUI the user is being asked if proteins that have no peptides in the spectral library should be discarded.
As far as I understand, there is no similar option in SkylineRunner, so all the proteins are kept, and that increases the size of .sky file by approximately 20Mb.
It would be nice to have an option/command to discard unreferenced proteins from the Skyline project to save the space and processing times.
Brendan: I think this should be the default, and we can add a flag that allows someone to keep everything, but I expect this to be an infrequently used option.