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Possibility to unlink the integration between light and heavy

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Possibility to unlink the integration between light and heavy carolin huber  2025-10-28 05:40
 

Their Skyline support team,

is there a possibility to apply different integrations (min and max rt for integration) for light and heavy without changing the transition list, that the quantification is performed with a surrogate?

Our department uses Skyline a lot for quantification, however, often different internal standards are used that require a different integration. We struggle with the use of the surrogate option, as this does not allow us a layout, where the peak can be shown in the same window together with the internal standard.

Thank you very much for your help,

Greetings from Zürich
 
 
Nick Shulman responded:  2025-10-28 16:03
Unfortunately there is no way to tell Skyline that a small molecule's heavy and light forms should have different integration boundaries.
For peptides, you can specify the "relative retention time" when you are describing a modification.
But there is no analogous thing that you can do for small molecules. For small molecules you have to use the "Surrogate Standard" feature when your internal standard has a different retention time from your analyte.

Note that if you are manually adjusting the peak boundaries you could give your internal standard different boundaries.
If you select a Transition in the Targets tree and choose "Transitions > Single" on the chromatogram graph, then, when you adjust peak boundaries, it will only affect the selected transition. In theory, you could do this for each of the transitions in your internal standard and thereby give the internal standard different integration boundaries.

Skyline intentionally makes it difficult to give a single transition different integration boundaries because this is usually not want to do. However, it would work in this scenario.
-- Nick