Optimization library for both collision energy and compensation voltage

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Optimization library for both collision energy and compensation voltage chi nguyen  2021-07-29
 

Hello Skyline team,

I am currently doing targeted proteomics on Altis with FAIMS and Skyline Version 20.2
I was wondering if it is possible to have a optimization library with both information about the optimized CE and optimized CV values or if I can import two separate libraries, one for CE and one for CV

Currently I can only use either CE or CV optimization library but not both...

thank you for your support

best,
Chi

 
 
Kaipo responded:  2021-07-29

Hi Chi,
A single optimization library can contain optimizations values of different types. From your screenshot, if you change the optimization type to Compensation Voltage and add the CV values, the optdb file should end up containing both CE and CV values.

Thanks,
Kaipo

 
chi nguyen responded:  2021-08-04

Hi Kaipo,

Thank you for your advice. It works fine for me to have both CV and CE information in one optimization library.

However, as I tried to perform PRM on Eclipse with FAIMS device. I can not export the isolation list with FAIMS information. I chose Thermo Fusion as instrument (see screenshot). There, I have no option "write Faims value" to choose. Do you know how I can do this? For now I added faims values externally, not in skyline.

Thank you
Chi

 
Kaipo responded:  2021-08-04

Hi Chi,

I guess we haven't added this option for the Thermo Fusion yet. Do you know what the column header should be (e.g. for Thermo Quantiva it is "FAIMS CV (V)") or do you have an example isolation list containing the FAIMS values?

Thanks,
Kaipo

 
chi nguyen responded:  2021-08-05

Hi Kaipo,

I attached a table with FAIMS information exported from the instrument method. I used eclipse with FAIMS.

regards
Chi

 
Kaipo responded:  2021-08-05

Hi Chi,
Thank you for the example. I will add this option for the Thermo Fusion.

Thanks,
Kaipo