Can you send me your DDA and this new PRM raw files? ("SA_LRA_10ug_150uLHW_081119_DDA.raw" and "SA_HL_LRA_10ug_Top14_131119_PRM.raw")
You can upload those files here:
Did your DDA run use the same chromatography settings as this new PRM run? That is, was the length of time the same, and was the physical column the same?
Now that you are using your DDA search results in your PRM Skyline document, there is a setting that now makes a difference:
Settings > Transition Settings > Full Scan > Retention Time Filtering.
You have it set to the default "Use only scans within 5 minutes of MS/MS IDs".
For a PRM experiment, you should probably always have that set to "Include all matching scans" since for PRM if you told the mass spectrometer to collect data at a certain time you would want to see that data in Skyline.
Also, if the chromatography in your DDA run were different than your PRM run, then you would definitely not want Skyline using the DDA times to restrict the length of chromatogram extraction.
I can see that in your DDA data you have a beautiful identification of QDGSVDFFR at 38.7 minutes.
Then, in your PRM run, Skyline has extracted a chromatogram from 33.7 to 43.7 minutes, and that chromatogram looks completely flat, indicating that nothing with that precursor m/z was present over that time range. I am wondering why that would be, which is why I would like to take a look at those .raw files.
Skyline is currently giving you only 3 transitions per precursor.
If you want Skyline to give you more, you can control that setting at:
Settings > Transition Settings > Library > Pick X Product Ions