i am posting this short observation since the exact same problem could not be found in the forum. We are using Skyline for a few years for targeted peptide analysis (thank you personally from us fro making that possible). We are using Triple QQQ (Agilent 6470) using the MassHunter Version Workstation Version 10.1. The Skyline version is the most recent one (Version 64-bit Skyline 126.96.36.1998). Windows version is10 Pro.
While following the standard protocol for the method development, the Step A seems always to function perfectly (update of retention time). While executing the following Step B for the optimization of the CE, the instrument always goes offline with the following message "there are errors in the method" (Slide 1, attachment).
We have loaded an example of the method for step B in the offline option of the Masshunter methods (Slide 2, attachment). It seems the problem is with a new column "primary" and the triggered option.
In the old version of skyline, we did not see this column while optimizing the CE and it functioned very well. We tried to remove the option "triggered chromatogram acquisition" in the transition settings - still we get same response and the instrument goes offline. We talked with Agilent support and they could not help us out. The "bug" remained even after the update of the Agilent MassHunter Version Workstation software yesterday.. We set in step B , the max. concurrent transitions at 50 delivering two methods for altogether 95 transitions and it did not function.
Can anyone help us?