Yes, please send us your files.

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.
The Share Document dialog gives you the option to include the raw data files in the .zip, which would be a good thing to do.
Alternative, you could zip up your Bruker .d folders in a separate .zip file and send them to us.

You can upload your files here:
https://skyline.ms/files.url

After we see your Skyline document and your Bruker data files we will be able to tell you why Skyline is doing what it's doing.
-- Nick

Hi Nick, I couldn't upload to the link you shared. could you please download from my google drive with below link?
https://drive.google.com/file/d/1nFDT3UdJKuiJMVuSXCO9HKF4RkV-MOyW/view?usp=sharing
thank you

Hi Nick, may I ask is there any update for this? thank you very much.

Oops. I forgot to take a look at this.

Can you send us some of the Bruker .d folders for this data such as "20251201_D90_genescript_2ng_PRM_S1-E1_1_4411.d"?

The usual reason that you do not see MS2 chromatograms in a PRM dataset like this is that there really were no MS2 spectra whose isolation windows matched the precursor m/z of the targets in your Skyline document.
The setting which controls how close the isolation target as reported by the mass spectrometer needs to be to the precursor m/z in the Skyline document is the "Method match tolerance m/z" setting on the "Instrument" tab at "Settings > Transition Settings". I see that this is set to 0.02 in your document. It's possible you would see MS2 chromatograms if you made that a larger number and then told Skyline to extract chromatograms again using the "Reimport" button at "Edit > Manage Results".

I see that on the "Ion Mobility" tab at "Settings > Transition Settings", "Use spectral library ion mobility values if present".
The two peptides in your document do not have any spectral library information (i.e. the "Library Match" window is empty), so I do not think that the ion mobility settings in your document are preventing you from getting MS2 chromatograms.
Having the wrong ion mobility settings could cause you to not see chromatograms, but I believe that would affect both MS1 and MS2 chromatograms, so that does not seem like it could be the cause of your problems in this document.

After I see one of your Bruker data files I will probably be able to tell you what is going on.
-- Nick

Hi Nick, Thank you so much for your reply. I have upload all the raw files to the same line. please take a look.
https://drive.google.com/drive/folders/1NRmTNOcRyyxFuVHK4bx7RJHqJgLiLgKi?usp=sharing

Thank you for sharing those .d folders.
When I look at that data using SeeMS.exe from ProteoWizard, all I see are MS1 spectra.
I do not see any MS2 spectra at all.

Do you have some other software that thinks there are MS2 spectra in there? Can you send us a screenshot of this other software so that we know what the data that we are not seeing should look like?
I am not the expert on ProteoWizard, but, sometimes, we can't see the data because it's not really the sort of mass spectrometry data that ProteoWizard is able to handle.

By the way, your document seems to have been created using Skyline 22.2. We always recommend using the released version of Skyline unless you are trying to reproduce results from older experiments.
The latest released version of Skyline is 25.1.
-- Nick