Can you send us your Skyline document and that .raw file?

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url

After we see that raw file we might be able to figure out why Skyline thinks it has a different polarity than you think it does.
-- Nick

Thank you for your response. I'll send you the Skyline raw data.

- Tae Ha

I uploaded the file '01192025_KTH' at file sharing

-Tae Ha

You should go to the "Full Scan" tab at "Settings > Transition Settings" and choose "PRM" in the MS/MS filtering Acquisition Method dropdown.

In your document, nothing has been chosen there so Skyline thinks you want to read the chromatograms from the raw file, as if this was an SRM experiment from a triple quadrupole mass spectrometer.
Usually when you do that you will get an error message saying the file "does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used."

However, your raw files do contain some SIM chromatograms so you are getting a confusing message telling you the polarity of those SIM chromatograms is incorrect for the transitions that are in your document.

However, if you go the Full Scan tab and choose "PRM" in the Acquisition Method dropdown Skyline will extract chromatograms from the MS2 spectra in those raw files.
-- Nick

It works well as you suggested. Thank you!

-Tae Ha