Unable to see any fragment ions in Skyline | clgunth2 | 2020-10-13 14:45 | |||||||||||||||
Hello - I created a test transition list with ions I can see in the raw mass spectra and imported into Skyline. When I imported the data, only the precursor mass is identified with the green circle next to the precursor name, even though the ions in my transition list were extracted from the raw file. The fragment ions don't have a red circle for being not detected but rather say "Chromatogram not available" if clicked on. I'm not sure if it's just not reading my data correctly or not. Again, these fragment ions were chosen directly from the raw spectra to test the workflow in Skyline, so they are present in the raw data. My data file contains only MS2 scans for one precursor. My goal is to be able to filter through a much longer list of theoretical fragments for one complex structure. I'm following similar to what I would do if I was filtering through a transition list with MS1 data except the data file contains solely MS2 scans. Thanks, |
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