LOD and LOQ calculation

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LOD and LOQ calculation a das  2024-11-16 04:49
 

Hi Nick,

I am doing ToF MRM for peptide quantitation in my sample with heavy-isotope labeled peptides.

  1. Can you please help to calculate LOD and LOQ in skyline?
  2. CV calculation?

Please share any tutorials having all these

Thanks
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Nick Shulman responded:  2024-11-16 08:43
Skyline offers a couple of ways to calculate limit of detection on the "Quantification" tab at "Settings > Peptide Settings".

1. If you have multiple blank samples, then you can choose to calculate the limit of detection as the blank signal plus either 2 or three times the standard deviation of the blanks.
2. Alternatively, if your regression method is "bilinear" then you can choose "Bilinear turning point" as the turning point of the bilinear curve.

For limit of quantification, you can specify the maximum CV and Bias on the "Quantification" tab at "Settings > Peptide Settings".
Skyline will examine each of the calibration levels starting at the most concentrated, and the limit of quantification will be determined by looking at each of the calibration levels starting at the most concentrated and stopping when a level is found which fails the criteria.

In Skyline-daily we are working on a new way to calculate limit of quantification, but at the moment I believe it has some mathematical problems so I would not recommend it.

If you want to know the CVs of your data, you can use either the "View > Peak Areas > CV Histogram" or "View > Peak Areas > CV 2D Histogram" menu items.
Alternatively, you can use the Pivot Editor in the Document Grid to calculate CVs.
There is some documentation showing how to calculate CVs here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor
Calculating CVs in the Pivot Editor was also briefly covered at around minute 38 in this recent webinar:
https://skyline.ms/project/home/software/Skyline/events/2024%20Webinars/Webinar%2023/begin.view?
-- Nick