Any algorithm differences regarding the extraction of SWATH and Scanning SWATH data by skyline.

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Any algorithm differences regarding the extraction of SWATH and Scanning SWATH data by skyline. Winnie  2022-03-15
 

Hi Skyline team,

Recently, I have extracted targeted peptide precursors from SWATH and Scanning SWATH files by Skyline. I am wondering if there are any algorithm differences about data extraction from SWATH and Scanning SWATH by skyline.

Best regards,

Winnie

 
 
Winnie responded:  2022-03-18

Hi Skyline,

Did someone give me any information about this question?

Best regards,

Winnie

 
Nick Shulman responded:  2022-03-19
I am not aware of anything in the Skyline code which was specifically written to deal with scanning SWATH.
Skyline always extracts MS2 chromatograms by looking at each spectrum and deciding which precursors in the document were contained in the isolation window for that spectrum. Skyline adds a point to the chromatogram of each transition belonging to those precursors.

I am not sure I understand exactly what scanning SWATH data looks like. I do not know how good of a job Skyline does when it extracts chromatograms from scanning SWATH data.

I am guessing that if you were to tell Skyline to extract chromatograms from scanning SWATH data, the intensity of the chromatogram points would fluctuate over the course of the scanning cycle since some of the spectra would have the precursor of interest in the middle of the isolation window, and some would have the precursor near the edge, and the edge effects would affect the measured intensity. One way to reduce these edge effects is to tell Skyline to only consider the middle part of the isolation window as actually having been isolated. To do this, go to:
Settings > Transition Settings > Full Scan
and use the Isolation Scheme dropdown to add a new Isolation Scheme where you have selected "Use results data isolation targets" and for the Isolation Width choose "Results with margin" and set the margin to the amount of the isolation window which you would want Skyline to exclude when Skyline is deciding which precursors were contained in the isolation window.

I have never seen scanning SWATH data, but if Skyline is not doing a good job with your data you can send us your data and we might be able to figure out something you can do to improve things.

-- Nick
 
Winnie responded:  2022-03-20
Hi Nick,

The results of peak extraction from Scanning SWATH data by skyline are ok. I just want to know any algorithm differences of the skyline to process Scanning SWATH and SWATH data. Thanks.

Best regards,

Winnie