If your compound is easier to find in some replicates than others, then we have a new feature called "Peak boundary imputation" which will help with that.
This new feature will be available in the next update of Skyline-daily.
You can read about it here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PeakImputation

However, it sounds like you're asking about a feature where you tell Skyline that a compound B always elutes right after compound A.
Unfortunately, Skyline does not really have any features to specifically help with that, but I have seen people talk about things like that at some Skyline User Group Meetings.

You might be able to get something to work just using the general "iRT" (indexed retention time) features.
You can read about iRT here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_irt

We might be able to give you better advice if we could see your data.
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
-- Nick

Hi Nick,

Thank you for your prompt reply.

To clarify, we are looking for guidance on using Skyline for retention time prediction in targeted metabolomics, specifically using a relative retention time (RRT) approach. Unlike the iRT method common in proteomics, we will use a single internal standard as a reference. We want Skyline to use the known RRT of a target compound and the observed RT of the internal standard to calculate the target's expected RT.

Chloe