How does skyline handle the origin when performing calibration

How does skyline handle the origin when performing calibration jrenders  2021-05-13

Hi there,
Pretty easy question I hope, but I couldn't find any documentation on this topic in previous requests:

I would like to understand how Skyline handles the origin when performing calibration of analytes. I noticed that in my calibration curves the regression line extends below my lowest accepted calibrator (and I am not accustomed to seeing this in MS quantitative plots). This got me thinking that perhaps skyline considers the origin when performing these calibrations. Typically, the choices for how to handle the origin are "Include", "Force", or "Ignore" (I usually use "ignore" in small molecule quantitation) but I cannot see any indication of what is used or how to change this setting in the "Molecule Settings" --> "Quantification" window. Thanks for any info!

Brendan MacLean responded:  2021-05-13

Typically, Skyline ignores the origin, unless you have chosen for your Regression fit "Linear through zero" in which case it will force the regression through the origin.

Interesting point, though, about "line extends below my lowest accepted calibrator". This sounds like you are expecting the lowest accepted calibrator to serve a function like LOD or LOQ. Skyline does have ways of calculating those values and including them in the plot. The regression line on the graph is just the regression line and no attempt is made to plot its ending, unless you use "Bilinear" option.

I find that I am not easily able to find an explanation of LOQ calculation in Skyline or even a screenshot of the calibration plot with the LOQ plotted. I will ask Nick to add one to the Skyline Wiki under Tips > Qantification.

Thanks for posting to the Skyline support board.