When your molecule has an internal standard, it is very important that the light and heavy versions appear under the same Molecule in the Targets tree.
That is, there are four levels of things in the Targets tree:
Molecule Lists
Molecules
Precursors
Transitions

A common mistake when importing a Transition List is to give a different Molecule Name to the light and heavy versions of the molecule.
The light and heavy things in your transition list should have the same Molecule Name.

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.

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

It would also be helpful if you could send us your transition list that you imported into Skyline if you have one.

After we see your Skyline document we will probably be able to figure out how to get things set up the way you want.
-- Nick

Hi Nick,
 
thanks for your answer and sorry for my delayed response, I only work part time.
I did the mistake to not name the molecules the same for light and heavy. I changed that and now it seems to work. Thank you :)
I have to wait for green light to upload the zip because I'm not sure if I'm allowed to share the data.
 
I hope you don’t mind but I have some small additional questions:
1) If I have multiple product Ions (quantifier and qualifier) is it possible to like select only the quantifier for calculations ?
2) In Analyst I have some infos in Sample ID and in Skyline it’s Sample Id, is it possible that it doesn’t get the Info because Id/ID is written different?
3) Also I have a screenshot, because we’d like to look at the peaks in fixed rt window, but somehow we can’t choose this option (I think we have to define it somewhere but we tried it at several settings and it didn’t work.
4) Is it possible to set a threshold for a minimum area or height for the peaks.
 
Thank you very much in advance and sorry for the rather simple questions
 
Kind regards and a nice weekend
Laura

1. You can mark a Transition as non-quantitative by right-clicking on it in the Targets tree and unchecking the menu item that says "Quantitative". When a Transition has been marked as non-quantitative its area will not be included in values such as "Total Area".

2. I believe that the "Sample Id" column that you can find in the Document Grid will only ever have a value if the raw file came from Thermo.
If you are able to convert your .wiff files to .mzML you can try to look at the .mzML file using a text editor and see if you can find the information you are looking for.
If you are able to find the sample information in the .mzML file, let us know, and we could make it so that Skyline reads that information from the same place.
But, I expect that you will not find any sample information in the .mzML file which means that Skyline would not be able to read it from your .wiff file either.

3. In order to be able to choose "Retention time window" for "Auto Zoom", you have to have a retention time predictor. You can do that on the "Prediction" tab at "Settings > Molecule Settings". The iRT tutorial is helpful for learning about retention time prediction:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_irt
With small molecules, people often do not want to set up a retention time predictor, but they do want to set the "Explicit Retention Time" for the molecule. The "Explicit Retention Time" is a column that you can display Document Grid and set, or you can right-click on Molecules in the Targets tree and choose "Modify" and specify an Explicit Retention Time there.

4. Skyline does not really have a feature of minimum threshold. If you want to remove all of the peaks where the area is less than a certain value then you could look at the "Molecule Transition Results" report in the Document Grid, filter down the set of rows to those matching certain criteria and use the "Actions" button at the top of the Document Grid to remove the peaks for the selected rows.
-- Nick