I am not sure I understand your question but this page has some diagrams showing how Skyline calculates background:
In general, we do not believe it is possible to determine LOD and LOQ by looking at the shape of chromatograms. The only reliable way to determine those numbers is to have a calibration curve, and see which concentrations can be distinguished from each other. This is because there are lots of different things going on in the sample and the mass spectrometer which contribute to variation in measured values, and the specific noise that you are able to see by looking at a spectrum or a chromatogram is only a small part of that total variation.
I am supposed to implement some features in the next version of Skyline which will implement Dr Lindsay Pino's technique for determining LOD and LOQ by looking at the calibration curves of random subsets of the calibration points. I am not sure where to find the latest version of that algorithm, but an early iteration of that is described here: