13C phenylalanine and second isotope abundance of unlabeled phenylalanine

13C phenylalanine and second isotope abundance of unlabeled phenylalanine Sam110  2022-05-10

Hello, I have a dataset with phenylalanine and isotopically labeled 13C phenylalanine which is only one mass unit from the unlabeled phenylalanine. I wanted to know if Skyline can subtract the value for the second isotope abundance of the unlabeled phenylalanine from the 13C phenylalanine?

Nick Shulman responded:  2022-05-10
I think the feature that you are asking for is what we have been calling "deconvolute overlapping isotope distributions".
This feature has been on my todo list for a long time, but we do not have any sort of estimate for when it might actually get implemented in Skyline.
Here is the todo item:

There is an external tool called "TurnoveR" which is available in the Skyline Tools Store. That tool is designed to figure out the rate constant of an isotope labeling experiment where you are feeding heavy labeled food to a live organism. I know that as part of what that tool does, it also does overlapping isotope deconvolution. I don't know whether there would be any way to use that tool to get the numbers that you want.
Here is a slide deck showing what the TurnoveR tool does:

Sorry that we have not yet implemented this feature in Skyline.
-- Nick