Dear skyline team,
When generating isolation windows list in skyline for DIA experiments, if you check "optimize window placement", do you think there is still a need to do 1 mz overlap margin at either side of the windows?
thank you
Abla Tannous
Brendan MacLean responded:
2018-01-23 10:01
We do not see the need for overlap with optimized window placement if you are measuring only charge 1-3 peptides. I did a DIA experiment on this with a Bruker TOF, and so no real decline in peptides detected or peak area CVs between optimized window placement and overlapping margins.
The MacCoss lab does all its DIA with Orbitrap mass spectrometers using optimized window placement and no overlapping margin.
Hope this helps. Wish we had a publication to point to on this question.