Hi Samuel,
To predict the retention times for these peptides you would need some kind of prior measurement of them, not necessarily DDA. You could run unscheduled PRM and search the resulting MS/MS spectra the way you would DDA. This is detailed in the "Targeted MS/MS (PRM)" tutorial.

Or, if you have already made some kind of prior measurements and you have iRT values for all of these peptides against the Pierce PRTC kit, then you can just measure those peptides on your chromatography, preferably in some kind of pooled background that mimics your intended sample. Having that one measurement of the standards on your chromatography combined with a fully populated iRT library/calculator would allow you to export a schedule PRM method with predicted retention times. This should be pretty well detailed in the "iRT Retention Time Prediction" tutorial, where you train an iRT calculator on a 30-minute gradient and then train it for a 90-minute gradient.

Maybe you could attach your Skyline document with your iRT predictor, using File > Share - Complete to create a .sky.zip file. That would give me a bit more to look at, and I could tell whether you have iRT values for your target peptides or whether you need to do a first measurement of your target peptides before you could hope to predict their retention times on your gradient.

Sorry, this got by me at first and it took a while to get you this response. I hope it helps somewhat. Happy to help more, if you can give more detail.

--Brendan