I am surprised that switching the Acquisition Method from "DDA" to "PRM" would fix this in your case.
The usual reason that doing that fixes things is that Skyline cannot extract DDA MS2 chromatograms unless Skyline has also been asked to extract MS1 chromatograms because Skyline uses the MS1 extraction windows to decide which DDA spectra to include in the MS2 extracted chromatogram.
However, in your screenshots I can clearly see that Skyline was extracting MS1 chromatograms, so I wouldn't expect that to be the issue.

If you feel like it, it might be helpful if you could send me your Skyline document and your .raw file.
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.
In the "Share Skyline Document" dialog there is also an option to include .raw files, or you could send us the .raw file separately.

If that .zip file and/or your .raw file are less than 50MB you can attach them to this support request. Larger files can always be uploaded here:
https://skyline.ms/files.url

It sounds like you have already figured out a solution to your problem so don't worry about sending us files unless you want to.
-- Nick

I will send over a .zip file in a second.

The file will contain a few raw data files, a Skyline file using the DDA, and a skyline file using the PRM.

One thing I did notice with the file "012_10ngL_20231128" the PFOS chromatogram is the while chromatogram when using the DDA for the precursor ion, but when you switch to the PRM and reimport you only get a partial peak for the precursor. Is there some setting when using the PRM that is causing the program to only extract part of the chromatogram data?

Hi Nick,

Might take a little time for you to figure out why there is the difference between use the DDA and PRM acquisition methods.

I was wondering if you had any insight as to why chromatogram peaks don't look the same between the two. For example, in DDA the chromatogram shows the whole peak, but when switched to PRM it only shows a partial peak sometimes. See attached images.

--Zack

When the acquisition method is "PRM" (or "DIA") and Skyline notices that the time range over which MS2 spectra were collected is less than the entire run, Skyline truncates the MS1 chromatograms so that they match the MS2 chromatograms.
The reason that Skyline does this is that it's the correct thing to do if you had a scheduled PRM method.

Skyline does not do this truncation if the acquisition method is "DDA". For this reason, we recommend that you use the "DDA" acquisition method for data like this.

The reason that you are not seeing any MS2 chromatogram for your molecule "PFOS" in the file "119_FB-20_20231128.raw" is that the "Explicit Retention Time" that has been set on that molecule (7.75) is outside of the time range over which there were MS2 spectra with matching precursors.
Skyline always discards chromatograms whose time range does not overlap with the explicit retention time.

The reason that you are seeing different behavior with the "DDA" acquisition method compared to "PRM" is that those two acquisition methods have different ways of deciding whether a particular spectrum matches a precursor.
The "PRM" acquisition method uses the "Method match tolerance m/z" value at "Settings > Transition Settings > Instrument" to decide whether the isolated precursor in the raw file is close enough to the m/z of the precursor in the Skyline document. In your document, the method match tolerance is 0.055m/z which is the default value.
When the acquisition method is "DDA", Skyline uses the MS1 m/z extraction window which is controlled by the "resolving power" setting at "Settings > Transition Settings > Full Scan".
There is an MS2 spectrum at 12.86 minutes which had the precursor 498.9397.
That value is close enough to 498.9302 so that it gets included in the PRM extracted chromatogram, but it is not close enough when the acquisition method is DDA.

-- Nick