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Individual Regression Options for Peptides/Precursors

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Individual Regression Options for Peptides/Precursors sascha  2022-02-10 08:34
 

Currently, you can define regression options for the document in "Settings > Molecule Settings > Quantification" that apply for all targets. However, the response of individual targets is not the same, thus you might need for example a linear regression without weighting for molecule 1 and a quadratic regression with a 1/x weighting for molecule 2, and so on.

After the last Skyline MS Online event, I was told that this is currently not possible in Skyline, and encouraged to report a feature request. It was suggested that these settings might be implemented in the document settings as "Explicit" molecule option. Since I do not have permission to open a new issue, I use this forum for this request.

If this request needs any more clarification, please let me know. I would be grateful for the implementation of this feature, since it is the only obstacle to replace commercial quantification software in our lab.
 
 
Nick Shulman responded:  2022-02-10 08:47
That sounds like it would be straightforward for us to implement.

Could you send us a Skyline document which has multiple different molecules that you would like to use different regression options on? Also, let us know what settings you would want to use with each molecule. It's always easier to implement features like this if we have a real world use case to look at.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
https://skyline.ms/files.url

-- Nick
 
sascha responded:  2022-02-10 13:53
Here you find a Skyline document with different molecules. Ideally, you would use a 1/x^2 weighting for each molecule except Amisulpride and Pipamperone, which should use no weighting at all.

In reality, each molecule can be calculated using a linear regression, but for the sake of an example assume that Melperone and Risperidone need a quadratic regression.

Additionally, each molecule uses an individual 3-point calibration curve with each of the calibrants not being derived from a dilution series. Is there any plan to implement such complex quantifications in the future?

I attached a summary of all quantification parameters in an Excel-Sheet.

Thank you so much for considering.
 
Nick Shulman responded:  2022-02-10 14:07
Thank you for sending that document.

Yes, Skyline supports documents where the concentrations of the different molecules in the external standards are completely unrelated to each other. Usually the "Analyte Concentration" that you can specify on the Replicate, combined with the "Concentration Multiplier" that you can specify on the Molecule is sufficient to specify what is going on.

If that's not sufficient, then you can use the "Explicit Analyte Concentration" which can be found on the Molecule Results in the Document Grid. You can use the binoculars search button at the top of the Customize Report dialog to find that column.

Is that what you were asking?
-- Nick
 
sascha responded:  2022-02-10 23:38
Yes! That was exactly what I was looking for!

Thanks a lot for your help and developing Skyline.
 
sascha responded:  2023-10-12 04:48
Dear Nick,

sorry for digging this up again. We are in the need of individual regression options, such as 1/x weighting for molecule A but not for molecule B. Currently, Skyline does not support explicit regression options. Would it be possible to integrate this into the software?

Best regards,

Sascha