I believe that you can control the length of the chromatogram that gets extracted by going to:
Setting > Transition Settings > Full Scan
At the bottom of that page, there are some options related to whether the chromatogram should be truncated, and I believe choosing the one related to predicted retention time will result in a shorter chromatogram.
After the chromatogram is extracted, Skyline looks for something that is shaped like a peak. The explicit retention time that you specify is a very strong hint as to where Skyline should find that peak, but, I believe, if the chromatogram is completely flat at that point, Skyline might choose a peak somewhere else. (We are trying to think of a way to make "explicit retention time" more explicit so that this never happens).
The area that Skyline reports is always going to be the area between two integration boundaries, and is not dependent on anything that happens with the chromatogram outside of these boundaries. Thus, even if you specify the "Explicit Retention Time Window". Skyline will still look for a peak that overlaps with that window, and will not integrate beyond the boundaries of the peak-shaped thing that Skyline finds.
If you want to actually tell Skyline the real start and end times over which it should integrated, you can use the menu item:
File > Import > Peak Boundaries
-- Nick |