Ratios not showing up in Document Grid

Ratios not showing up in Document Grid amanda bayless  2023-06-27 10:50
Hi, I am doing a small molecule targeted quantification, and I can't seem to get the ion ratios to show up in the document grid file. Underneath any columns relating to ratios (ie Ratio light to heavy) it reads #N/A. All of the data has imported ok and the ratios do appear in the graph function. Do you have any suggestions on how to resolve this issue?

Thank you,
Nick Shulman responded:  2023-06-27 10:57
Can you send us your Skyline document?
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:

The usual reason that ratios like that do not show up is that there is no molecule which has a heavy and light precursor. That is, the heavy and light precursors ended up in separate molecules.
There are four levels of things in the Targets tree: Molecule List, Molecule, Precursor and Transition.
In order for ratios to be calculated by Skyline, there needs to be a heavy and light Precursor which both have the same Molecule parent.

It's also possible that something entirely different is going wrong. We will be able to figure it out when we see your Skyline document.
-- Nick
Nick Shulman responded:  2023-06-27 11:23
Thank you for sending that Skyline document.
Yes, the problem is that your heavy and light Precursors are under different Molecules in the Targets tree.

I imagine that you added those things to your Skyline document by using either the "Edit > Insert > Transition List" or the "File > Import > Transition List" menu item.
If you send us your transition list, we can tell you how to change it so that you will get one Molecule with a heavy and light Precursor. I think the transition list probably needs to have a "Label Type" column, but I am not sure.
-- Nick
amanda bayless responded:  2023-06-27 11:46
Yes, I imported it as the following (373 and 375 are the quantifiers):
Name    m/z    RT    precursor charge    RT window    Product    product charge    Label
Glucose    511.2    3.06    1    2    175.1    1    light
Glucose    511.2    3.06    1    2    373.2    1    light
Glucose_1    517.2    3.06    1    2    175.1    1    heavy
Glucose_1    517.2    3.06    1    2    375.2    1    heavy
Brian Pratt responded:  2023-06-27 12:10
You just need to change "Glucose_1" to "Glucose" to make Skyline understand that these are labeled versions of the same molecule.
amanda bayless responded:  2023-06-27 12:14
Thanks, I should've thought to try that!