It sounds like you intended to attach a file to this support request, but nothing actually got attached.
This often happens if the file you were attempting to attach was larger than 50MB which is the maximum attachment size.
If the file you wanted to send us is larger than that you can upload it here:
https://skyline.ms/files.url

It would be helpful to see your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including libraries and extracted chromatograms.
-- Nick

Hi Nick,

Thanks you for pointing it out. I have uploaded the file in the given link.

When Skyline extracts chromatograms from DDA data, the chromatograms tend to have long straight lines that connect the times where a matching MS2 spectrum happens to have been acquired.
Also, if there were no matching MS2 spectra then the MS2 chromatograms will be missing entirely.

I see that the "MS/MS filtering Acquisition Method" on the "Full Scan" tab at "Settings > Transition Settings" is set to "PRM".
When the acquisition method is PRM, the setting which controls how closely the isolated m/z needs to be to the precursor m/z is the "Method match tolerance m/z" setting on the "Instrument" tab of Transition Settings (which is currently set to the default 0.055 m/z).

If you do want to see chromatograms extracted from DDA data, we recommend choosing "DDA" as the acquisition method.
When DDA is the acquisition method, any spectrum which is contained within the precursor isotope envelope (controlled by the "Isotope peaks included" and "Precursor resolving power" full scan settings) will be used for the extracted chromatogram.

The other reason that you should choose "DDA" instead of "PRM" is that, when the setting is "PRM", Skyline will truncate the MS1 chromatograms so that they match the MS2 chromatograms. Skyline does this because it's the right thing to do for scheduled PRM methods, but it's not what you would want for DDA data.

When you choose "DDA" as the acquisition method, the MS2 chromatograms will be displayed as dotted lines which indicates that Skyline will not use them for quantification.

DDA MS2 chromatograms are not very useful in Skyline, but we added support for them so that you would have something to click on in the chromatogram graph to bring up more information about the MS2 spectra.
-- Nick

Thanks for the suggestion. I have changed it. I understood that since i used the DDA, so MS2 will not be useful. But then to create the isolation list for PRM method out of it, will it still contain the information about mobility and mass of all of transitions even though I can not see it?

Isolation lists do not contain any information about fragment ion m/z's-- just precursors.

I see that your spectral library does have ion mobility information in it.
However, the ion mobility library that you have on the "Ion Mobility" tab of "Settings > Transition Settings" only has information about a few peptides.

What you need to do is go to the "Ion Mobility" tab at "Settings > Transition Settings", and choose "<Edit current...>" in the Ion Mobility dropdown.
In the "Edit Ion Mobility" dialog, you should push the "Import" button and tell it to import ion mobility values from your spectral library "CDome_DDA_lib_only precursor".

After you do this, you will be able to use the "File > Export > Isolation List" method to export an isolation list for Bruker timstof.

By the way, I see that you are using Skyline 24.1.
The latest released version of Skyline is 25.1. We always recommend using the latest version unless you are trying to reproduce results from old experiments.
I am not sure whether anything has changed between these versions in any area related to this.
-- Nick

Thanks Nick. It is working in this way. I will update the version soon.