There are a couple of things that might be going wrong:
1. Take a look at the Retention Time Filtering setting at the bottom of:
Settings > Transition Settings > Full Scan
Your settings there might be telling Skyline to truncate the chromatograms a certain number of minutes away from the MS/MS identification or the predicted retention time.
2. If you have told Skyline to extract chromatograms from MS1 and MS2, and Skyline will sometimes truncate the MS1 chromatograms so that they cover the same time range as the MS2 chromatograms. The reason that Skyline does this is that it's the correct thing to do if you are doing a scheduled PRM run. However, there are some cases where you do not want Skyline doing that.
One way to prevent Skyline from truncating the MS1 chromatograms like that would be to change the Transition Settings Full Scan MS/MS Filtering Acquisition Method to "DDA".
After you change your transition settings, you will need to tell Skyline to extract the chromatograms again by going to:
Edit > Manage Results > Reimport
3. Take a look at the "Min Time" and "Max Time" settings at:
Settings > Transition Settings > Instrument
You might have told Skyline to stop extracting chromatograms at the max time.
If none of these ideas solve the problem, you should 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.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
If you're sending us your Skyline document you should probably also send us one of your .raw files.