Most of the time it does nothing unless you have a spectral library which includes peak boundaries, which at this point would come from only 2 tools: EncyclopeDIA and OpenSWATH, both DIA tools. Though, it could be expanded in the future to include other tools which assign integration ranges to identifications, but we will always make it an option whether you want to use the other tool's peak boundaries or ones newly calculated by Skyline.

But, again, this does not impact the vast majority of libraries used with Skyline.