Skyline stopped integrating in the middle of the peak

Skyline stopped integrating in the middle of the peak dtran25992  2022-09-20

I was using Skyline small molecule to quantify this molecule ran on Shimadzu LCMS 9030 QTOF. The data was run using DDA method then raw data was imported to skyline for quantification.
I had a standard curve and a few actual samples that are run in triplicates
However, for some of the replicates, Skyline just stopped extracting/integrating in the middle of the peak (red box).
I went back to the Shimadzu's software and try manual extracted ion chromatogram of that peak and saw it's there in full.
I've never seen anything like this before, hopefully somebody can help,
Thank you very much,

Nick Shulman responded:  2022-09-20
If Skyline has extracted chromatograms from both MS1 and MS2 spectra, and Skyline notices that the extracted MS2 chromatogram covers a shorter time range than the MS1 chromatograms, then Skyline will truncate the MS1 chromatograms so that they are the same length as the MS2 chromatograms.
The reason that Skyline does this is that it is the correct thing to do in scheduled PRM experiments.

That is the most likely reason that your MS1 chromatograms are truncated like that.

One way to prevent Skyline from doing this would be to go to:
Settings > Transition Settings > Full Scan
and change the MS/MS Acquisition Method to "DDA".
When the MS2 acquisition method is "DDA", Skyline will not truncate the MS1 chromatograms, but also, Skyline will treat the MS2 transitions as "Non quantitative" and their chromatograms will be drawn in dotted lines.

It's possible that something else is going wrong.
If it does not seem that your matching MS2 spectra cover a different time range than the MS1 spectra then 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.

Files which are less than 50MB can be attached to this support request.
You can upload larger files here:

-- Nick
dtran25992 responded:  2022-09-20
Hi Nick,
You are absolutely right. I went to the raw data and saw that there was only 1 MS2 scan and the MS1 chromatogram was truncated right after that. I changed the full scan transition settings to DDA like you said and it works! Thanks a bunch!