I see that at "Settings > Transition Settings > Full Scan" you have MS1 filtering enabled, but do not have MS2 filtering enabled.
That means that Skyline will only be extracting chromatograms for the precursor.
In order for something to be recognized as a precursor by Skyline, the precursor and product m/z's need to be the same number.
In the attached screenshot, the precursor is 164.0717 and the product is 166.0863, so Skyline would only extract chromatogram points for that transition from MS2 spectra, but MS2 chromatogram extraction is disabled by the settings at "Settings > Transition Settings > Full Scan".
Do you know which is the correct m/z for that molecule?
If you want to add precursor transitions to your document, you would usually specify the precursor formula and the product formula in the same way.
In your transition list, the precursor is specified with the formula C9H11NO2, but the product is specified with the m/z 166.0863. If those two things are supposed to be the same, then I would recommend that you remove the column "Product m/z" and instead have columns "Product Formula" and "Product Adduct" and put the same things in those two columns as you have in the columns "Precursor Formula" and "Precursor Adduct".
It's possible that I am misunderstanding what you want your transition list to look like. If you were hoping to get MS2 chromatograms, let me know what you were hoping your transition list would be.
-- Nick |