CE optimize method XML parameter issue with Agilent 6495B qqq

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CE optimize method XML parameter issue with Agilent 6495B qqq wangqingok  2019-01-18
 

Dear Skyline Group Experts,

I am using Skyline to optimize a set of over 10k peptides, and would hope to do it in a high-throughput way. I started with a batch of 200 peptides.

After I exported the method with a template method and transitions of these peptides (one method per peptide), and I put them into the worklist of the 6495B qqq, and after I initiate the run, it shows in the MassHunter Acquisition Logbook as "
Error AcqEng MSQQQ_1: Failed to download parameters to the instrument. Invalid XML string. Failed to process the child elements in element [timeSegments]
Failed to process the child elements in element [timeSegment]
Failed to process the child elements in element [scanSegments]
Failed to process the child elements in element [scanSegment]
Failed to process the child elements in element [scanElements]
The Maximum number of [scanElement] elements allowed in this collection is 99".

However, when I just export the transitions as with CE optimizations and then copy-and-paste these transitions into the template method, it runs flawlessly in MassHunter on 6495B. I am wondering if the Skyline is actually not compatible with the parameters required by Agilent 6495B therefore the template method is not properly loaded and outputted through Skyline??? Thanks a lot!

 
 
wangqingok responded:  2019-02-25

Hi Skyline expert team, could you please let me know if there is a solution to this problem? We are optimizing a large number of peptides and this issue is blocking us from doing optimization using skyline. Any help is much appreciated! Thanks a lot!