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FAIMS CV optimization - Please Report "NA" in the Ion Mobility filtering settings for peptided with removed peak

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FAIMS CV optimization - Please Report "NA" in the Ion Mobility filtering settings for peptided with removed peak Tobi  2024-03-20 03:52
 

Hi Skyline Team,

when using skyline to optimize FAIMS CV, that works in principle when having having data with multiple CVs and going via
Settings/Transition Settings/Ion Mobility/Ion Mobility Library/Add/Use Results

From there the optimized CV values can be copy&pasted and used elsewhere, I have not managed any other way to export the optimized CV values.

However, when some precursors or peptides had their peaks removed (chromatogram, righclick, remove peak), I would expect those to be listed with "NA" as optimized CV value, but they are simply missing from the ion mobility library window. This creates mismatches with the table of optimized CVs I would like to make.

The copy&paste is fine, but please keep the numbers of peptides and precursors consistent with the target list, that would be a great improvement.

Best, tobi
 
 
Nick Shulman responded:  2024-03-20 06:43
There is a column in the document grid called "Library Ion Mobility".
Does that column have the number that you were hoping to be able to copy?

You could create a Report with Precursor and Library Ion Mobility columns and then there would be #N/A values for the precursor with missing ion mobility values.

If you need to learn more about creating custom reports in the Document Grid you should look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

The Document Grid is the usual way to get lists of numbers out of Skyline.
-- Nick
 
Tobi responded:  2024-03-23 04:34
Thanks Nick for the quick help,

the library ion mobility works as you suggested, I just needed to figure out that the "library" is an ion mobility library which is separate from the spectral library.

In just a few cases the optimized CV is not quite the CV from the MS1 chromatogram apex as in the screenshot, is that within functionality or a potential issue? Unfortunately I cannot share data at the moment.

Best,
tobi