Issue 962: Find CCS values for targets not found in an IMSDB library without changing existing values

Assigned To:Brendan MacLean
Opened:2023-06-26 10:03 by Brian Pratt
Changed:2023-06-26 10:03 by Brian Pratt
2023-06-26 10:03 Brian Pratt
Title»Find CCS values for targets not found in an IMSDB library without changing existing values
Assigned To»Brendan MacLean

"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.

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."

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.