Thanks for posting to the support board and for sending the screenshot in email. Probably it would still be easier for others to understand with the screenshot. I have to admit that I find a number of things puzzling about that screenshot.
Maybe you could post a PowerPoint slide deck with the original screenshot and a shot of your Transition Settings - Full-Scan tab.
It looked like you had signal on your precursor and precursor M+1, but somehow Skyline had given those transitions red dots in the Targets view, which seems to indicate that it felt the precursors were not coeluting with the fragment ions, but that didn't make much sense me either, because the peak shapes looked similar to my eye.
You might try Settings > Integrate All and see if that turns all of the dots green. It should only leave transitions with no signal at all with red dots.
Beyond that, I also see that the precursors have less intense chromatograms than the fragments, which is also a bit unusual. I suppose if you used a detector other than Centroided (e.g. Orbitrap) then you might get lower signal if you used a very high resolving power for the precursor (higher than the data would support) and a more appropriate resolving power for the fragment ions. Essentially, the higher resolving power narrows the extraction range in the m/z dimension and you could be excluding signal with a very narrow resolving power.
So, it might be good to include screenshots of what you see in the Full-Scan plot when you click on the apex points for both your most intense fragment ion and your most intense precursor. i.e. what the source spectra, from which the peaks were extracted, look like.
Finally, in your email, you asked about the vertical red lines with the number 29 at the right-hand side. These represent your points across the peak, i.e. where spectra were collected along the elution profile you have integrated. These are only shown when you have a transition selected in the Targets view and not when you have the peptide or precursor selected, but if you prefer not to see them at all, there should be an option to turn off this annotation in View > Transitions or right-click > Transitions.
Thanks again for posting to the support board.