Apologies if this question has been answered before and i missed finding it.

Using the small molecule CE optimization approach (skyline-daily version). The analyte peak wasn't picked up automatically in some of the repeats so i wanted to manually adjust integration parameters.

I receive an error message "failure attempting to modify the document, Duplicate or out of order peak in transition Ion [xxx]". As seen on attached screen.

Do you have more information what this error refers for? I have run the CE optimization method with a transition list that i manually transformed from the one i exported from Skyline (on a SCIEX QTRAP, the one i exported would give me errors, but i used the same CE values). Import the results files as you detail in the tutorial, so it would create a new file CE optimization. And the CE steps appear with different colours. Here no 5 different method file, only 1, but i injected 5 times to test repeats.

Thank you and let me know if you need more information.

Virag