Exporting phosphopeptides from MaxQuant into Skyline to visualize phospho spectrum

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Exporting phosphopeptides from MaxQuant into Skyline to visualize phospho spectrum Niyatti  2021-09-03
 

Dear MacCoss Lab, I'm working on enriched phosphopeptides and would like to import the identified phosphopeptides (filtered) from MaxQuant to Skyline to visualize the phospho spectrum or phosphosite spectrum. so is there any way I could do that in the skyline? If, yes then could you please help me out with the same.

 
 
Nick Shulman responded:  2021-09-03
Here is the web page which lists the types of peptide search results that Skyline knows how to read, and which files you need:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

That page says the for MaxQuant you would need the files: msms.txt, evidence.txt, mqpar.xml, modifications.xml
(I've never seen a "evidence.txt" file, so that file must not actually be required).

The way to get peptide search results into Skyline is by using the menu item:
File > Import > Peptide Search

There are many tutorials to help you get started with Skyline. If you are wanting to work with MaxQuant search results, it might be helpful to start with the DDA MS1 tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search

I am not sure I understand what you mean by "visualize the phospho spectrum". Skyline is a great tool for extracting chromatograms from all types of liquid chromatography mass spec data. Skyline is not a very good tool for looking at spectra. When we want to look at individual spectra in raw files, we often use "SeeMS.exe" which you can get if you install ProteoWizard.
https://proteowizard.sourceforge.io/download.html

Hope this helps,
-- Nick