"Copy Data" on Chromatogram

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"Copy Data" on Chromatogram SChen  2026-02-05 07:57
 

Dear Skyline Team,

I would like to get the maximum and minimum intensity values within the integrated peak boundaries for each transition. From what I can tell, the only way to get this is by right clicking on the Chromatogram panel and select "Copy Data". But I can only get one peptide at a time using this method. Is there a way to get the data for all precursors in Document Grid?

Thank you,
Shimin

 
 
Nick Shulman responded:  2026-02-05 08:28
You could create a custom report that includes the "Raw Times" and "Raw Intensities" columns and then look at the intensity values between the integration boundaries and find the minimum and maximum.
If you have a large Skyline document, a report with this chromatogram data might be too large.

You can get close to the values that you want by looking at the "Height" and "Background" values for each transition.
Here is a diagram showing how Skyline calculates the height of a peak:
https://skyline.ms/home/software/Skyline/wiki-page.view?name=tip_peak_calc

The "Height" of the peak is the maximum intensity minus the background level of the peak.
The background level of the peak is defined by Skyline to be the minimum of the intensity at the start and end of the integration boundaries.
If the peak does not dip down in the middle, then the background level is equal to the "Background" value that you can see in the Document Grid divided by the peak width.
If the peak does not dip down in the middle then this background level is also the minimum intensity between the peak boundaries.

Therefore:
Min Intensity = Background / (End Time - Start Time)
Max Intensity = Height + Background / (End Time - Start Time)

Note that the "Height" is calculated by Skyline by looking at the "interpolated" chromatogram where the intensity values have been interpolated in the time dimension so that the retention times are evenly spaced. For this reason, the Height reported by Skyline is always a little less than the actual height of the chromatogram that you would see looking at the raw data because it always involves averaging data from two nearby points.

You can read about custom reports here:
https://skyline.ms/home/software/Skyline/wiki-page.view?name=tutorial_custom_reports
-- Nick
 
SChen responded:  2026-02-05 09:51

Nick,

Thank you for the detailed explanations!

I think using the Interpolated intensities and Interpolated times values is the best option for me. My run was acquired using a triggered-based method (SureQuant). It looks like there is a different way of calculating background for triggered-based method based on this document, which is probably the reason why I am seeing 0s in the Background column in Document Grid.

You are right about the large file size. I was able to process it in R to extract the min and max intensities within the peak boundaries. I ended up using the Interpolated intensities and Interpolated times to get the same numbers as ones in "Copy Data".

Thanks again for your help!
Shimin