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CCS Calculation Option for Only One Feature

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CCS Calculation Option for Only One Feature aburnell  2023-05-29 11:40
 
I do lipidomic analyses on an LC-IMS-MS platform and am often looking to add new lipids to our in-house library. However, I always have to make a new Skyline document in order to calculate the ccs value of a new lipid without changing my previously calculated results. I thought it would be helpful to request an option to only recalculate/calculate one transitions rather than all the lipids on the transition list. I find that it does alter my results if I try to calculate all the ccs values again.
 
 
Brian Pratt responded:  2023-05-30 09:08
This does sound useful. Can you expand on this idea a little? Are you wanting to obtain CCS by manually specifying an ion mobility value, or be re-analyzing data to determine one? Having done so, are you wanting the chromatogram to be reevaluated? And, is this in the context of a spectral library, or an ion mobility library?

If you can lay out your ideal scenario step by step, that will help us figure out how to help you better.

Thanks for using the Skyline support board!

Brian Pratt
 
aburnell responded:  2023-05-30 10:07
Hi Brian,

My ideal scenario would include being able to have Skyline calculate ccs values for select features only. I would like to be able to add a new lipid to an already established transition list (of a skyline document that I have already mostly analyzed) and have Skyline calculate the ccs value of that lipid only. This would be in the context of an ion mobility library.

Currently, when I want to get skyline to calculate a ccs value for a new lipid I am looking for (and never have before), I create a new transition list with just the lipid(s) I am looking for with the information I do have (molecule group, precursor name, precursor formula, precursor adduct, product name, product formula,    product adduct, and high energy DT offset) and I create a new Skyline document with that list and my data files. In that doc, I go to settings > transition settings > ion mobility > ion mobility library > add, then I create a new library just to get the ccs value. If I do this same procedure in a document of an already established lipid transition list with ccs values, the ccs values for the lipids I already have calculated are incorrect in the new library.

Does this make sense? Please let me know if it doesn't because I am still learning. I appreciate you taking this into consideration!

-Amie
 
Brian Pratt responded:  2023-05-30 12:40
So perhaps:
 - a new control alongside the "Use Results" button in the Edit Ion Mobility Library window,
 - probably a checkbox labeled "Missing precursors only" (or something like that),
 - which when checked indicates to Skyline that it needs to examine the document for things that don't appear in the library, and deal only with those.
 
aburnell responded:  2023-06-01 06:19
Yeah mostly! I think there should also be a way to indicate both missing from the library and no explicit user input of ccs from the transition list too.