LC-MS/MS data file input for Skyline 20.1.0.155

support
LC-MS/MS data file input for Skyline 20.1.0.155 avaldiviezo  2020-07-29
 
I've been using Skyline for a few months to analyze data files generated by Ion Mobility - Mass Spectrometry and the software works very well. Recently, I have been trying to use Skyline to analyze data generated by Liquid Chromatography - Tandem Mass Spec, but I cannot see any peaks when I upload the data files after importing my transition list. Is there a particular way I need to set up the molecule/transition settings or transition list settings in order to analyze LC-MS/MS data?

Any help with this issue is greatly appreciated!

Thanks,
Alan
 
 
Nick Shulman responded:  2020-07-29
Can you 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.

Otherwise, you can upload it here:
https://skyline.ms/files.url

We might be able to figure out what is going wrong by looking at this .zip file, or you might also need to send us some of your raw files.

If you would like, you could also post a picture of what you are seeing.
-- Nick
 
avaldiviezo responded:  2020-07-29
I added explicit retention times to the transitions and now I am able to see chromatograms. However, I would like to see abundance for each compound too.

Thanks,
Alan
 
Nick Shulman responded:  2020-07-29
If you want to get lists of numbers out of Skyline you should take a look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick