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peak picking of directed DDA

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peak picking of directed DDA ssedigh2  2025-02-13 12:06
 

Dear Skyline Support team ,

I am trying to set up a SureQuant method , I have done a survey run_directed DDA on my internal standards and have imported the raw files into skyline . I was wondering if skyline offers a tool to for peak picking ? or should I import into PD and use CHIMERYS ?

Best,
Sogol
 
 
Nick Shulman responded:  2025-02-13 12:52
I am not sure I understand your question.

There is some information about using SureQuant with Skyline here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=TriggeredAcquisition

You can perform a DDA peptide search in Skyline. Here is a tutorial showing how to do that using Skyline's built-in search engine MS Amanda:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search

If you have done a peptide search in another tool you can use those search results to build a spectral library. Here is a tutorial that can show you how to do that:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search
-- Nick