Hi Edit,
Sorry for the wait on a reply. I am sure this must just be a bug. We will have a look. You will likely have to use Skyline-daily to get the fix, though, until our next major release.
The unmeasured peptides should not impact your model, but you can use Edit > Refine > Remove Missing Results to get rid of them before running a model to be sure, and just to clean up your document.
When I have problems like this seeing the prediction line and window when I feel it should be there, I usually start with View > Auto-Zoom > Both. Sometimes it shows that the prediction is just very far from the chosen peak or even the extracted time range, if chromatogram extraction was based on something other than the prediction.
Thanks for reporting your issues.
--Brendan |