Hi Skyline team,
I would like to confirm how skyline treats a fragment ion that is produced from multiple precursor ions of the same peptide when the data is acquired with MSE. Without the use of IMS it is not possible to discern from which precursor the fragment ion is being produced due to the lack of quadrupole isolation.
When the integrated fragment area is summarized for the peptide and a transition for the same fragment exists in two (or more) precursors, is the area of this "repeated" transition summed twice (or more) or does Skyline recognize it is a repeated value and only counts it once?
As always, thank you for your time and help.
Sincerely,
Juan C.