Can you send me one or more of your .raw files?
Files which are less than 50MB can be attached to these support request.
You can always upload larger files here:
https://skyline.ms/files.url

The usual reason that you do not get any MS2 chromatograms is that there really were no MS2 spectra in the .raw file which matched the precursor m/z's in your Skyline document.

I see that the MS/MS filtering Acquisition Method at "Settings > Transition Settings > Full Scan" is set to "PRM".
"PRM" means that an MS2 spectrum will contribute to the MS2 chromatograms of the precursors whose m/z is within the Method match tolerance m/z on the "Instrument" tab of the Transition Settings.
Your method match tolerance m/z is the default value "0.055".

If your instrument method had incorrectly calculated the precursor m/z values of your peptide, you might still be able to rescue the dataset by changing the method match tolerance m/z to a higher number and then using the "Reimport" button at "Edit > Manage Results" to tell Skyline to extract chromatograms.

After I see some of your .raw files I will probably be able to tell you exactly what is going wrong.
-- Nick

After I ran the experiment with internal calibration matched ions were then populated in the document. So, I guessed this should be the mass accuracy issue as you expected. Could you please confirm that this was the case? I've attached the raw files named SST.zip as you suggested.

Thank you very much!
Kittinun

Thank you for sending those raw files.

It looks like you acquired MS2 spectra for all of the heavy precursors in your document and none of the light precursors.
Also, it looks like the m/z's of the isolation windows in the .raw file are all exactly 0.1 m/z higher than what Skyline has calculated the m/z's of the heavy precursors to be.

You should go to "Settings > Transition Settings > Instrument" and change the "Method match tolerance m/z" to a higher number such as "0.2".
After you do that, you can use the "Reimport" button on the "Edit > Manage Results" dialog to tell Skyline to extract chromatograms again.
All of your heavy precursors will then have MS2 chromatograms.

If you want to delete all of the light precursors from your document you can go to:
Refine > Advanced
and choose "light" in the "Remove label type" dropdown.

-- Nick

From your inspection, I tried to work around the method and found that if I set the Xcalibur method mass offset = "0" or reported mass = "original mass," the problem was gone. Thank you so much! Also thanks for the remove label tip!

Regards,
Kittinun