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noise level of a peak

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noise level of a peak heyang  2025-03-13 09:40
 

Hi Skyline Team,

We are a public forensic laboratory and use Skyline to interpret LC MRM results. As our samples can come from unknown environments (e.g. a body fluid stain on a piece of clothing) being able to evaluate noise is important.

To get a reasonable measure of noise contributed by potential contaminating substances, we would like to measure all mass spectrometry data for 30 seconds before and after the signal peak. Is it possible for Skyline to access and report average intensity from these two 30 second intervals so we can average them and use them to calculate S/N?

Thanks,
Heyi
 
 
Nick Shulman responded:  2025-03-13 12:57
There is no way to get Skyline to report a number like that.

I know there have been discussions about changing the way that Skyline calculates background by looking at the region before and after the integrated peak, but nothing has changed about Skyline's background calculation in many years.
There is a page which illustrates how Skyline calculates background here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tip_peak_calc

You could certainly export the chromatogram data yourself from Skyline and write software outside of Skyline to analyze that data.
One way to export chromatogram data would be to create a custom report which includes the "Raw Times" and "Raw Intensities" columns.
You can learn about custom reports here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick
 
heyang responded:  2025-03-17 07:34
Thank you, Nick and it is very useful. Heyi