"No Base Peak Chromatogram Found" when trying to integrate DDA data

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"No Base Peak Chromatogram Found" when trying to integrate DDA data jarrod a roach  2024-03-11 08:45
 

I'm trying to integrate small molecule DDA data from a Q-exactive plus in negative ionization mode. I made my transition list using MS1 and MS2 values that I know exist in my results, but when I import my results it does not recognize a base peak chromatogram. Does anyone have an idea as to why this might be happening? I've attached my skyline file. Thanks!

 
 
Nick Shulman responded:  2024-03-11 09:43
The "No base peak chromatogram found" message is showing because you have chosen "Base Peak" under the either "View > Transitions" menu item or the "Transitions" item on the chromatogram right-click menu.
You should choose something else such as "View > Transitions > All".

The real problem that I think you are asking is why hasn't Skyline extracted chromatograms for any of your transitions.

I see that you have chosen "DDA" as the "MS/MS Acquisition method" at "Settings > Transition Settings > Full Scan".
When "DDA" is the acquisition method, Skyline will not extract chromatograms unless Skyline has also been told to extract chromatograms for the precursor. So, one thing that you could do is change the Acquisition Method to "PRM", and then tell Skyline to extract chromatograms again by using the "Reimport" button at "Edit > Manage Results".

Alternatively, you could some precursor transitions to your Skyline document.
The easiest way for you to add precursor transitions to this document would be to right-click on one of the precursor m/z values in the Targets tree and choose "Pick Children".
When the child picker window appears, check the checkbox next to "precursor".
After you have added some precursors to your document you will need to tell Skyline to extract chromatograms again using the "Reimport" button at "Edit > Manage > Results".

If you still are not able to see extracted chromatograms in Skyline you should send us your .raw file and we can figure out exactly what is going on.
Files which are less than 50MB can be attached to this support request, but your .raw file will probably be bigger than that so you can always upload it here:
https://skyline.ms/files.url
-- Nick
 
jarrod a roach responded:  2024-03-11 12:20
You are correct, I was was wondering why I didn't have extracted chromatograms. I switched the acquisition method to PRM and reimported my transition list/results and that got me the result I was looking for. Thanks!