Can I set up Skyline to exclude quantification results when scan numbers are too low?

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Can I set up Skyline to exclude quantification results when scan numbers are too low? wangn2  2022-05-20
 
Hello there!
I got a question about the scan numbers (or also called "points across peak"?) in Skyline.
When the concentration of a target peptide is too low in a sample, usually the scan numbers of the chromatograph peak would be very small, say 3-6.
Can I exclude such peaks for quantification, meaning, ask Skyline to report intensity as N/A or 0, for peaks that have scan numbers less than a specific number, e.g. six?

Thanks a lot!
 
 
Nick Shulman responded:  2022-05-20
You can use the Document Grid to find all of the rows satisfying a particular criteria, and, after you have selected your rows of interest, you can use the "Actions" dropdown at the top of the Document Grid to remove the peptide peaks for the selected rows.

If you would like to learn more about the Document Grid you should look at the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

Skyline never pays attention to Points Across the Peak when detecting or choosing peaks, so there would be no way to get Skyline to do this sort of filtering for you automatically.
In general, when the question comes up as to how to change the criteria that Skyline uses for picking peaks, we mention the Advanced Peak Picking Models tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_peak_picking
But, even with a custom trained peak picking model there would be no way to get Skyline to do exactly what you are asking.
-- Nick