The graphing package that Skyline uses does not know how to draw a curve from an equation. For this reason, whenever the calibration curve is not a straight line (either because it's a quadratic equation or because you are looking at a logarithm plot), what actually gets plotted on the graph are one hundred points along the line.

When you right-click on the calibration curve graph and choose "Copy Data", one of the columns of data that you get are the points along the calibration curve, and there are either going to be two points or one hundred points in that column, depending on whether Skyline expects the curve to be plotted as a straight line.

The values in that column are what you would get if you plugged different X values into the calibration curve (y=mx+b) equation.

There will also be separate columns for each of the sample types ("Unknown", "Standard", etc.) that you are currently displaying, since they get plotted on the graph with different symbols.

If you want to draw your own calibration curves, I would recommend that you use a Custom Report to export the values that you need.

The y-axis values being plotted are the Normalized Area (Peptide Results > Quantification > Normalized Area) and the x-axis values are the Analyte Concentration specified on the Replicate. If a Replicate does not have a specified Analyte Concentration, then the X-value is what you would get from applying the inverse of the calibration curve to the Normalized Area.

You can find the equation for the calibration curve under Peptide > Calibration Curve.

If you want to learn more about Reports in Skyline you can take a look at this tutorial:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick