Are you using regular Skyline version 22.2 or Skyline-daily?
In Skyline 22.2, there is a report called "Transition Results" which will have one row for each transition and each replicate. The "Fragment Ion" column in the report will tell you which transition the row is for. Skyline considers each of the different precursor isotopes to be a different transition, so the "Fragment Ion" values will be "precursor" for the monoisotopic precursor, and "precursor [M+1]" for the M+1 isotope, etc.
In Skyline-daily, the "Transition Results" report is hidden when you are in small molecules mode.
If you want to be able to use the Transition Results report you could do the following:
1. Use the "View > User Interface > Mixed" menu item to switch to Mixed mode.
2. Choose "Manage Reports" from the "Reports" dropdown at the top of the Document Grid.
3. Use the mode selector dropdown in the top right corner of the Customize Report dialog to change the mode of the report to "Mixed".
After you do that, the Transition Results report will be available in all of Skyline's user interface modes.
Also, the captions of the columns in the Transition Results report will change so that they say "Molecule" instead of "Peptide".
Does this answer your question?
If this does not answer your question then I might have misunderstood what you are asking. If that's the case you should send us 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 extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url
-- Nick
document grid.PNG
result grid.PNG
230415_Apollo_SmallMolPOS.zip