After chromatograms have been extracted, Skyline will display one of three symbols next to items in the Targets tree.

The meaning of the symbols next to Transitions depends on whether there is a checkmark next to the "Settings > Integrate All" menu item.

If there is a checkmark next to the Integrate All menu item, then the symbol next to each Transition will be green checkmark () if a peak was detected within the integration boundaries, and it will be a red "X" () if there was no peak detected between the integration boundaries.

If there is no checkmark next to the Integrate All menu item, then the symbol next to each Transition then there is the further requirement in order to receive a green checkmark that the apex of the transition's peak must be within a quarter of a peak width away from the apex of the largest peak in the peak group. There is also the requirement that the shape of the peak be similar to the shape of the other peaks.

At the Precursor and Peptide or Molecule level, the symbol will be a green checkmark () if all of the Transitions below it in the Targets tree have a green checkmark next to them. The symbol will be a yellow triangle () if at least half of the Transitions below it have a green checkmark. The symbol will be a red "X" () if fewer than half of the Transitions below it have a green checkmark.

The decision about which color symbol appears next to these items is based on the peak shape in the currently selected replicate.