If you go to:
Settings > Molecule Settings > Quantification
there are some options for telling Skyline how to calculate the lower limit of quantification (LOQ) and lower limit of detection (LOD).

For the limit of quantification, you can tell Skyline the maximum bias and CV. The bias tell Skyline to find the calibration level at which the points are withing X% of where they should be on the fitted calibration curve. The CV requires that you have multiple replicates at each calibration level, and tells Skyline to find the lowest calibration level where the CV is lower than the percentage you specify.

For limit of detection, Skyline offers ways of calculating it based on the measured amounts in the replicates that you have designated as blanks.

Also, if you have chosen "Bilinear" as the "Regression fit", then you can choose to calculate the LOD as the bilinear turning point. The "Bilinear fit" is something that we developed in the MacCoss lab where the linear regression is split into two parts: a horizontal part, and an angled part, and the limit of detection is taken to be the point where those two lines cross.

I am not sure whether this is covered by any of the tutorials that we have.
-- Nick