Lipodomics: How to apply single calibration curve (done with one representative molecule) to all members of a lipide class??

Lipodomics: How to apply single calibration curve (done with one representative molecule) to all members of a lipide class?? StefanW  2021-02-15

Because of the diversity of lipids they are normally separated in group, which share a common structural motive, like head groups etc. Typically these groups shares a common MS2 fragment.

The LipidCreator tool is very helpful in creating the corresponding transition lists.

For quantification it is usually to generate a calibration curve with one of the group member (i.e. PS (18:1, 16:0) ). Subsequently these calibration curve is used to quantify all group members. For this purpose the "slope" of PS(18:1,16:0) has to be assigned to all PS species (i.e. PS(20:0,16:0) or PS(16:1, 18:1) etc etc).
To my knowledge, such a assignment is unfortunately not possible in Skyline. Or ???

Inclusion this feature will procreate skyline to a unique and outstanding lipid my mind....

Thanks a lot for a comment on this support case.


Nick Shulman responded:  2021-02-15

There is currently no way to tell Skyline to use one molecule's calibration curve in order to calculate the concentration of a different molecule. You would have to do this sort of calculation in some external tool like Microsoft Excel.

Can you send us an example of a Skyline document that you would like to do this in? It's easier for us to figure out how to design new features like this if we can see a real world example where it would be used.

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. Otherwise, you can upload it here:

-- Nick
StefanW responded:  2021-02-18
Dear Nick,

as requested, I send you a copy of a representative project with

a.) Dilution of defined and odd lipids (10ng/ml to 10000ng/ml)
b.) A lipid extract from E.coli with a lot of defined and common lipids.

The task will be to quantify all PEs (PE16-19) in the extract with the calibration curve made from the standard (PE(15:0,18:1))

Thanks a lot for your support and efforts.


StefanW responded:  2021-03-01
Dear Nick,

I asked for your understanding for my impatience, but can you already estimate when you will be able to take a look at the problem?

Thank you for your help

Best Regards

Nick Shulman responded:  2021-03-02
We will start figuring out which features to include in Skyline 21.2 after Skyline 21.1 ships. That will happen sometime in May 2021.

-- Nick