Peptide Identification using DIA SWATH Data

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Peptide Identification using DIA SWATH Data gomesrja  2022-10-17
 

Good morning

I have a question...How to I know each peptide and proteins are considered identified and present in a sample using DIA SWATH data?

I am doing an untargeted global analysis of all possible proteins in the library. Is the library match peptide score?

Many Thanks,

Ricardo Gomes

 
 
Nick Shulman responded:  2022-10-17
One way to get False.Discovery Rate (FDR) values for your DIA data would be to add decoy peptides to your document, extract chromatograms, train a peak scoring model. After you do all that you can use the Document Grid to look at the "Detection Q Value" numbers.

Here is the tutorial for training peak scoring models:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_peak_picking

Here is the Document Grid tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

--Nick