Skyline version 24.1.0.199

support
Skyline version 24.1.0.199 anhdao darcy  2024-10-15 09:17
 

Hello,

I have just downloaded a new version of Skyline. However, in the "peptide setting" section of the new version, the normalization method shows no option of "Ratio to Heavy." Do you know why? Please see the attachment for more information.

Thank you
Anhdao

 
 
Nick Shulman responded:  2024-10-15 09:42
The logic for deciding whether "Ratio to Heavy" to appear in the list of choices for "Normalization Method" on the "Quantification" tab at "Settings > Peptide Settings" has not changed since about December 2021.
I think Skyline looks at whether any of the modifications listed in the "Isotope modifications" list at "Settings > Peptide Settings > Modifications" has a checkmark next to it.
If none of those isotope modifications has a checkmark next to it, then you will not be offered "Ratio to Heavy" as a normalization method.

There might be some limitations in this logic: if you have used the "Edit > Modify Peptide" menu item to explicitly give a peptide some heavy modifications then you might have some heavy peptides in your document even though no modifications in the Peptide Settings have a checkmark next to them.

It would be helpful if you could send me your Skyline document so that I can see whether a change needs to be made to Skyline's logic for offering normalization methods.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick