How could I see the mass spectrometry in the right window?

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How could I see the mass spectrometry in the right window? 1240470751  2022-03-19
 

Dear Skyline Team,
I'm a new user for this sophisticated software. The question I want to inquiry is that I was puzzled on how to see the Ion pair information and mass spectrometry of every peptide to theoretically select the best one for the MRM after I input the protein sequence and acquire a series of selected peptides as well as their ion information.
Thanks,
Zhichao

 
 
Nick Shulman responded:  2022-03-19
It looks like you have successfully told Skyline about the peptides that you are interested in.
The next step in Skyline would usually be to use the menu item:
File > Import > Results
in order to extract chromatograms from one of the raw data files that came from your mass spectrometer.

Skyline is only useful for extracting chromatograms and calculating peak areas. If you would like to do something else with your mass spectrometry data, such as look at spectra, Skyline is not the right tool. If you install ProteoWizard, you will get a program called "SeeMS.exe" which is a little better than Skyline for looking at individual spectra, but still probably not as good as the software which came with your mass spectrometer.
You can install ProteoWizard from here:
https://proteowizard.sourceforge.io/

There are many helpful tutorials on the Skyline website.
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials

Which type of mass spectrometer do you have?
If you have a triple quadrupole mass spectrometer, then it might be a good idea to start with the Targeted Method Editing tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_edit

If you have a full scan mass spectrometer, then maybe you should start with the MS1 full scan filtering tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering
 -- Nick
 
1240470751 responded:  2022-03-19
Thank you so much!