You can always "rescue" a peak classified as "truncated" by moving the integration boundary at the edge one point inward. That is, the current criteria Skyline uses to classify a peak as truncated are:
- An integration boundary is placed at one extreme end of the available chromatogram (i.e. first or last point in the chromatogram)
- The integration boundary at the chromatogram extreme is more than 1% of the peak height higher than the other integration boundary.
I agree that #2 is too stringent and should probably be raised to something like 10%. I am the one who wrote this algorithm, but I have since seen peaks I also felt were not really truncated that get classified as truncated, and 1% of the peak height now seems to me like it could easily just be caused by noise variation. So, probably we will change this.
For now, if you want to manually correct this, you can simply move the integration boundary one point in from the edge. Skyline also gives you a number of tools to find which peaks have been classified as truncated, including an advanced option under Edit > Find and the Document Grid.
This is covered in great detail starting on page 11 of the Processing Grouped Study Data tutorial:
Good luck. Thanks for reporting the issue. Look for a change to a higher percentage of the peak height in the future.