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Replicate comparison - collision energy optimization

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Replicate comparison - collision energy optimization a b heijnis-2  2024-09-17 04:07
 

Hey! For our proteomics project we are using the automation tool to connect Skyline with Masshunter from Agilent. Therefore we have two questions.

Recently, we have compared the export methods that we made by going through the steps manually and doing it with the automation tool. Luckily, the results were completely the same!
However, Skyline comes up with the starting point for CE optimization, using step size and step count. We would like to further optimize with the results of the first experiment as an starting point. How could we approach this?

Secondly, when processing our results in Skyline in the replicate comparison, the different CE are always displayed as step (-2, -1, 1, 2 etc.). See figure in the attachments.
We would like to know whether it is possible to have the CE settings shown in de legend as there are many differences between peptides.

Thank you in advance!

Alexander
 
 
Nick Shulman responded:  2024-09-17 14:07
There is no way to get Skyline to display anything other than the step number for those optimization steps. It would be a useful feature if Skyline told you the actual collision energy but Skyline does not currently do that.

If you want to use a different value other than the value from the linear equation as the starting point when you export your collision energy method, you can set the "Explicit Collision Energy" values for your peptides.
I gave a description of how to do that here:
https://skyline.ms/announcements/home/support/thread.view?rowId=64806

-- Nick