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Peak picking and non-quantitative transitions

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Peak picking and non-quantitative transitions roman sakson  2022-02-02 08:38
 

Dear Skyline team,

I perform MRM measurements with 50 - 100 peptides across many samples, where I have selected a subset of quantitative transitions but I also keep non-quantitative ones in the Targets list to facilitate visual inspection. When starting with such a "mixed" transition list in a new, empty Skyline document, does the "quantitative" property of transitions influence initial peak picking by Skyline right after raw data import?

Thank you,
Roman
 
 
Nick Shulman responded:  2022-02-02 08:58
The "Quantitative" property on Transitions is not supposed to affect peak scoring at all.
When we added this feature, our thinking was that you would want to keep these transitions in the document so that they could help with peak picking, but they would not be included in things like "Total Area".

If you want to tell Skyline to pick the peaks again, you can go to:
Refine > Reintegrate
and push "OK".

As far as I know, marking transitions as quantitative or non-quantitative will not affect the peaks that Skyline chooses. So, if you were to select all your transitions and mark them all quantitative, and then reintegrate, the contents of the "Peak Boundaries" report in the Document Grid will remain the same.
-- Nick
 
roman sakson responded:  2022-02-02 12:04
Great, thanks Nick!