Peptide Identification using DIA SWATH Data

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:

Here is the Document Grid tutorial: