Scheduling window does not change

Scheduling window does not change roberthardt  2021-04-16

Dear Skyline-team,

I am using the current version of Skyline Daily and noticed a bug when changing the scheduling window with an iRT predictor. No matter which value(2, 4, 5 min) we set the window to, Skyline keeps the window at 10 min. I first thought that this might be purely a visualization error, but the constant 10 min windows are also apparent in the inclusion lists we export. We also tried fixing the problem by exporting the whole project ("share") and opening it on a different computer, but the problem persisted.

Hope you can have a look at the attached project and help us with this issue.



roberthardt responded:  2021-04-16

Dear developers,

I found the problem myself. Apparently there are two places where one can set the scheduling window. First in the "Prediction" tab of the "Peptide settings" menu and second in details panel "Edit retention time predictor" of the chosen predictor. Interestingly, the setting in the submenu overrules the setting in the prediction tab.
Is there a reason for having this separate places for setting scheduling windows? What is the actual difference between both?

Best regards


Brendan MacLean responded:  2021-04-16

Hi Robert,
The window in "Edit Retention Time Predictor" is the window when the retention time is based on a predictor (either SSRCalc or more often iRT in modern experiments). The window in the "Prediction" tab is based on prior measurements, if you have them. Finally, it is also possible to override both of these in the Document Grid with the "Explicit Retention Time Window" field.

Sorry, this is a bit confusing, but the expectation is that windows based on prediction would need to be wider than windows based on a prior measurement. You can see the windows based on prior measurement at work in the Targeted Method Refinement tutorial.

Hope this helps for future use. Thanks for posting to the Skyline support board.