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Problem of viewing CE optimization result for some transitions (small molecules)

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Problem of viewing CE optimization result for some transitions (small molecules) William  2018-07-02 21:19
 

Hi Brendan,
I have imported the CE optimization result to Skyline (small molecules) and encountered some strange issues. I can see CE optimization results for most transitions except two (dG-A and G-dA), both with precursor of 634.28. Could you please have a look what's wrong with the file or settings? I checked it in Xcalibur and seemed ok (different CE steps were there).
Thanks,
WIlliam
 
 
Brian Pratt responded:  2018-07-03 10:15
Hi William,

Can you explain a bit more about what you are expecting to see (maybe using screenshots from Xcalibur)? I seems like some replicates work better for some transitions, but that's the nature of CE optimization (I'm assuming each replicate is a different CE?). I'm probably just not understanding the issue.

Also, may we also see the raw data files in question?

Thanks,

Brian Pratt
 
William responded:  2018-07-03 15:13

Hi Brian,
CE001 and 002 are two files for split CE optimization method, CE003 is scheduled SRM CE optimization (including all transitions).
I should expect 7 chromatograms (7 CEs, shown in attachment) for each transition. However for transitions from precursor of 634, I can only see one chromatogram (shown in attachment), I wonder what's the reason for it (where's other 6 CEs)? I have also attached three raw files FYI.
William
 
Brian Pratt responded:  2018-07-03 15:49
OK, I see what you mean, thanks. I'm looking into it.

Brian
 
William responded:  2018-07-12 15:39
Is there any progress?