Precursor exclusion m/z window

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Precursor exclusion m/z window vanyabangera  2024-08-21 22:11
 

Dear Skyline team,

We have found a response regarding query on Precursor exclusion m/z window. However, we were not able to understand importance of "Precursor exclusion m/z window" instead the option to use "DIA precursor exclusion window".

Thanks in advance

Vanya

 
 
Nick Shulman responded:  2024-08-21 23:19
If the MS/MS Acquisition Method specified at "Settings > Transition Settings > Full Scan" is "DIA" and you have an isolation scheme which lists the windows (that is, the isolation scheme does not say "Use results data isolation targets") then the "Precursor m/z exclusion window" text box gets replaced by a checkbox "Use DIA precursor window for exclusion".

My understanding is that there are some mass spectrometers which cannot detect fragment ions whose m/z is inside of the window that is being fragmented.
That is, any product ion whose m/z falls within that window will continue to get fragmented until its m/z is no longer in that window.

There is a bit of a discussion about how that works and why there needed to be two different settings here:
https://skyline.ms/issues/home/issues/details.view?issueId=333
-- Nick