Failed to export method for CE optimization

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Failed to export method for CE optimization benoit fatou  2020-06-08
 

Dear Skyline Team,
I tried to export a MRM method to perform CE optimization and I have got this error message (see attached file).
Could you please help me solve this issue?
Thanks,
Best,
Benoit

 
 
Kaipo responded:  2020-06-08

Hi Benoit,
Would you mind sharing the Skyline document that is giving you this error (File > Share...)?

Thanks,
Kaipo

 
benoit fatou responded:  2020-06-08

Please find attached the Skyline document.
Thanks for your help,
Benoit

 
benoit fatou responded:  2020-06-09

Hi Skyline Team,
I was wondering if you have any update on my issue.
Thanks,
Best,
Benoit

 
Kaipo responded:  2020-06-09

Hi Benoit,
Sorry I forgot to ask earlier - can you also provide the method template file?

Thanks,
Kaipo

 
benoit fatou responded:  2020-06-09

Hi Kaipo,
Please find attached the method file and the exported transition list from Skyline.
Let me know if you need anything else,
Thanks,
Benoit

 
Kaipo responded:  2020-06-09

Hi Benoit,
I am able to reproduce this bug which occurs when exporting an optimization method and will make a fix for the next Skyline-daily.

Thanks,
Kaipo

 
benoit fatou responded:  2020-06-09

Thanks Kaipo!
can you tell a bit more about this issue? I am interesting about that.

Thanks,
Benoit

 
Kaipo responded:  2020-06-09

Hi Benoit,
When exporting a Shimazu method, we provide a numeric ID for every set of precursors. When we give the list of transitions to the Shimadzu library, it expects that these IDs are in order, but they aren't in this case so we need to correct the order before we give them to the library that writes the method.

Thanks,
Kaipo

 
benoit fatou responded:  2020-07-03

Hi Skyline Team,

My previous issue about exporting the method for CE optimization is partially solved.
The good thing is there is no error message about the export and the realization of CE optimization.
The bad thing is now that the several precursors for the same peptide are merged into an event.
Do you think it is possible to keep a single precursor ion (with the associated transitions) into an unique event?
I attached 2 screen shots without the issue and with the issue on combining 2 precursors into a single event.

Let me know if it is not clear.
Thanks for your help,
Benoit

 
Kaipo responded:  2020-07-07

Hi Benoit,
It is a little more tricky to do it this way, but I am looking into a way to do it.

Thanks,
Kaipo