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High Energy DT Offset

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High Energy DT Offset sxu374  2022-10-20 14:17
 

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
 
 
Brian Pratt responded:  2022-10-20 15:32

Hi Anne,

Can you provide an example where this is not working for you? We would need to see the transition list and the mass spec data itself.

Thanks for using the Skyline support board!

Brian Pratt
 
sxu374 responded:  2022-10-21 10:29

Hi Brian,

Sure, I can provide you the .sky file, raw data, and transition list. I wonder if there is a way to upload the raw data file privately.

Thanks,
Anne
 
Brian Pratt responded:  2022-10-21 12:31

Anything (Dropbox etc) that works for you is fine, just email me at bspratt @ proteinms . net.

Brian
 
Brian Pratt responded:  2022-10-24 11:37

Hi Anne,

Thanks for providing your data.

The difference in the "works" and "does-not-work" data sets is that the former has Transition Settings > Full Scan > MS/MS Filtering set as All Ions DIA and the latter is set as PRM.

Currently Skyline only uses the High Energy Ion Mobility Offset value for All Ions DIA, but clearly this is not what you were expecting.

I suppose this raises the question: is there any full scan MS2 setting for which one would not want the high energy ion mobility offset behavior?

Brian
 
sxu374 responded:  2022-10-24 12:32

Hi Brian,

Thank you so much for your fast turnover and really appreciate your help!

This makes sense to me that this feature only supports All Ions DIA so far. Regarding your question, I think all MS2 settings will face the same Ion Mobility shifting issue and need the High Energy Ion Mobility Offset function for correct alignment. It will be very beneficial if the Skyline updates and enables this function to all MS2 settings in the near future.

Thanks,
Anne