Several people have noted that it is difficult to re-optimize transitions for which the optimization based on the linear equation failed to capture an apex in the CE dimension. It should be made possible to run subsequent rounds of optimization including only the precursors for which an optimal value was not clearly measured.
This is a little complicated due to the need to know the central CE value from which the optimization range was generated. Currently that central value is assumed to be the one predicted by the current linear equation for CE in the document settings. In order to make this second round optimization work, Skyline might need to snapshot best measured CE values for certain precursors into the document settings, to be correlated with the CE optimization data during import.
We could certainly make this work, and it would be a great improvement to the CE optimization functionality. Unfortunately, it is not a top priority at the moment.
Steve S., who originally requested this also adds the ideas below for an future round of development on CE optimization.
One final note: if you do at some point implement more CE functionality, it would be nice to also
-read in the CE from raw files, to allow previously optimized CE values (from other software/manual optimization) to be stored in Skyline.
-have the option to display individual CE values when viewing data in skyline (alongside the fragment mass, intensity, retention time).