Hi Skyline support team,
I have some data acquired from Agilent 6560 IM-QTOF. I noticed that for some analytes, the IM drift times of the fragments are lower than their precursors, leading to unsuccessful alignment. In a literature, I found a function called "HighEnergyDTOffset", which could set in skyline transition list. This function indicates how much the fragment drift times could be lower than their precursor. I added the "HighEnergyDTOffset" column to my transition lists of different batches of data. Something interesting is that this function only works for certain transition lists. In other transition lists I loaded, the IM drift time window applied in MS/MS spectra was the same as the precursor, not having any drift time offset at all. I wonder if there is a guidance on how to set "HighEnergyDTOffset" correctly, or if there is any restriction on how the data is acquired by MS (AIF, PRM, etc.) in order to enable this "HighEnergyDTOffset" function.
Thanks,
Anne