Hi Ben,
1. Set in Peptide Settings - Prediction tab under Use measured retention times when present, Time window field.
2. I am told this is supposed to be for Normalized Collision Energy, and that our lab may be using 25 for this value across the board. It looks like the developer on this feature chose to use the function in Skyline that calculates an actual CE for each precursor based on linear equations assigned in the Transition Settings - Prediction tab, used for SRM transition lists. This is not correct for this column on the Q Exactive, however, and we will fix this in the future. You should be able to use Excel to fill this column with whatever normalized CE works best for you.
Thanks for your feedback.
--Brendan |