Surrogate External Calibration

Surrogate External Calibration jrenders  2023-07-12 10:44

Hi there,
I have a unique challenge I was hoping Skyline would be able to help me solve. I have a compound I would like to quantitate but standards do not exist this compound. I have an isotopologue standard of the compound and have a calibration curve using that isotopologue. However, I am unable to find a way to quantitate a compound against a calibration curve if they do not share the same precursor mass. Is this possible? For context: I have standards for the light variant of the compound (no heavy atoms) and I have a standard for the triply deuterated version, however, in my unknown samples I will be observing a version of the compound that has 6 heavy carbons despite not having a standard for this 13C6 variant. Thanks for any insight.

Nick Shulman responded:  2023-07-12 13:17
I don't think there is any way to do what you want to do in Skyline but if you send us your Skyline document we might be able to figure something out.

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.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:

It sounds like what you would like to be able to do in Skyline is just tell Skyline what the slope and intercept of the calibration curve for a particular molecule is. You would just copy those numbers from the calibration curve that you have. Unfortunately, Skyline does not have any feature like that, so you would probably have to be doing this sort of calculation in some other program such as Microsoft Excel.
-- Nick
jrenders responded:  2023-07-13 09:30
Thanks for your reply, Nick. It seems like you understand my request perfectly. Didn't think it was possible, but wanted to check. Currently, I am already doing as you suggested: using Skyline to produce the regression for the calibration curve I have and then using the slope and intercept to calculate for the isotopologue in excel by using the ratio to the same internal standard.

I haven't built out the Skyline doc for the exact set of compound I am researching, but I have a test document I have uploaded, where I am trying to get Skyline to quantitate testosterone glucuronide using the curve for androsterone glucuronide (both of which are normalized to a heavy variant of androsterone glucuronide). File has the title of this request in the description.