I would need to see your .raw files to tell you why your MS2 chromatograms are not showing up.
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

When the MS/MS Acquisition Method on the "Full Scan" tab at "Settings > Transition Settings" is "DDA", an MS2 spectrum will be included in the extracted chromatogram if the isolated m/z is within the extraction window for the MS1 chromatogram. That extraction window is controlled by the "Mass Accuracy" setting in the "MS1 filtering" section on that Full Scan tab. For this reason, yes, it is possible that the 10ppm mass accuracy that you have specified is preventing any DDA MS2 spectra from being included in the extracted MS2 chromatogram. If you change that to a higher number and then use the "Reimport" button at "Edit > Manage Results" you might see some MS2 chromatograms.

Skyline is not a very good tool for looking at MS2 spectra in DDA experiments. Skyline is very good at extracting chromatograms, but, with DDA data, the same precursor is not sampled at reliable intervals so DDA MS2 chromatograms tend to have long straight lines connecting the times where a matching MS2 spectrum was found.
-- Nick

Dear Nick Shulman,

thank you for the reply!
I followed your suggestions, but I still cannot find MS2.
I should mention that I have only one or two data points for MS2 (e.g., 91.0542 from 248.2373 of BAC8) because the Full scan/ddMS2 method triggers MS2 scan when the precursor ion signal is strongest (please see the attached file, 2025-05-08_BAC-Mix.....).

Also, after changing the mass accuracy in the transition settings, and re-importing my data, I received an error message about the MS2 time window (see the second attachment). Therefore, I added an "Explicit retention time window" for 1 (minute) in the transition list, but it did not help.
I guess Skyline missed the MS2 data points due to their small number?

I have attached two raw data.

Thank you so much for looking into my problem!

Best regards,
Yohan Seol

When the MS/MS Acquisition Method is "PRM" or "DIA", after Skyline has finished extracting the MS2 chromatogram, Skyline truncates the MS1 chromatogram so that it covers the same time range as the MS2 chromatogram. The reason that Skyline does this is that it's the right thing to do when you have a scheduled PRM method and have told the mass spectrometer the time range over which to collect MS2 spectra for your particular analyte.

When the MS/MS Acquisition Method is "DDA", Skyline does not do this truncation of MS1 chromatograms based on the MS2 chromatogram.

The error that you are seeing about discarding chromatograms is happening because the "Explicit Retention Time" value has been set on your molecules. Skyline discards all chromatograms that do not overlap with the specified Explicit Retention Time value. For this reason, you should only set the Explicit Retention Time if you are sure that the mass spectrometer will acquire spectra over that time range and that your molecule's peak will overlap with that time.
You can use the "Molecules" report in the Document Grid to change the Explicit Retention Time values.
You can learn more about the Document Grid in the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick