When you have missing MS2 chromatograms like that, the reason is usually that Skyline did not find any MS2 spectra where the isolated precursor matched the m/z of the precursor in your Skyline document.
Sometimes you can work around this by choosing a larger number for the "Method match tolerance m/z" at "Settings > Transition Settings > Instrument", or sometimes the problem is that the isolation scheme at "Settings > Transition Settings > Full Scan" is not correct.
Other times, the problem really is that the mass spectrometer never collected any MS2 spectra which isolated the correct m/z because the instrument method was wrong.

If you would like, you can send us your Skyline document and one or more of your raw 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.
You can also package one or more of your Bruker .d folders into a .zip file.
If those .zip files are less than 50MB you can attach them to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick

Hello Nick,

I tried the following recommended settings:

"Method match tolerance m/z" at "Settings > Transition Settings > Instrument", or sometimes the problem is that the isolation scheme at "Settings > Transition Settings > Full Scan" is not correct.

Unfortunately, still couldn't see the transition peaks.

The possible problem that "the mass spectrometer never really collected any MS2 spectra which isolated the correct m/z because the instrument method was wrong" seems unlikely since the recorded MS2 with the transition ions can still be seen in the raw data attached along with the zip file.

I have uploaded the zip file "240108_Neg_PL mixture_PLA2 Before Digestion.sky.zip" at https://skyline.ms/files.url.

Regards,
Dhanwin

Thank you for sending those files.
It seems that the reason that the MS2 chromatograms do not show up for that molecule (m/z = 830.5913) is that the Explicit Retention Time has been specified for that molecule to be 14.3 minutes, but the first MS2 spectrum with a precursor of 830.5913 occurs at 14.33 minutes.
If you change the Explicit Retention Time to be blank, or change it to a larger number such as 14.4, and then reimport your results, then you will see MS2 chromatograms for that molecule.

This behavior seems like a bug. I will ask around and see whether we can fix this. We do get a lot of support requests where the Explicit Retention Time is a cause of chromatograms being unavailable.
For now, I would recommend changing that Explicit Retention Time value so that it is within the range of the MS2 spectra that were collected for that precursor.
-- Nick

Hello Nick,

Thank you for the feedback. I will implement the suggested changes.

Best Regards,
Dhanwin