All of what Nick says is true, but there is also a "Peptides > Internal Standard Concentration" value which can be set in the "Peptide Quantification" default report. So, yes, it is peptide-specific. We generally do not recommend using this value for single-point internal standard calibration (analyte concentration = standard concentration * analyte area / standard area). Though, we recognize that many people still do this. So, we made it possible in Skyline.
Instead, we would recommend that you use external calibration with either a multi- (calibration curve) or single-point external calibrator. Look for videos of lectures by Andy Hoofnagle on this, like this one:
With external calibration the internal standard is use for normalization only, and Skyline does not require any knowledge of its concentration. The (analyte area / standard area) ratio is used to calibrate against the external curve or single-point.
So, while I think what you are asking for is possible in Skyline, we would recommend you consider external calibration instead, which is also very flexible, as Nick described.
Thanks for posting to the Skyline support board.