Thanks for sending your Agilent .d files.
It sounds like you know a couple of the transitions that you want to monitor, and you are hoping to use Skyline to discover some more transitions.
Skyline is a great tool for extracting chromatograms. Skyline is usually not considered a very good tool for looking at spectra.
The program which we have which is better for looking at spectra is called "SeeMS.exe". That program gets installed when you install ProteoWizard. You can install ProteoWizard from here:
https://proteowizard.sourceforge.io/download.html
You can use Skyline to extract chromatograms from your data.
You mentioned in email that your precursor has m/z 158.1, and your product ions have m/z 141.00 and 95.00.
The way to get that information is copy the following text to the clipboard:
PrecursorMz |
PrecursorCharge |
ProductMz |
ProductCharge |
158.1 |
1 |
141 |
1 |
158.1 |
1 |
95 |
1 |
In Skyline, you can do:
Edit > Insert > Transition List
and paste in the text that you have on the clipboard.
You also need to tell Skyline that you want to extract chromatograms from MS2. To do that, you go to:
Settings > Transition Settings > Full Scan
and about halfway down
set "Acquisition Method" to "PRM"
and set "Product Mass Analyzer" to "QIT"
and at the very bottom choose "Include all matching scans".
After you have done that, you can save your document and then tell Skyline to extract chromatograms by going to:
File > Import > Results
-- Nick