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XCMS / Howto re-integrate with new rtborders?
I'm running lipids on C18 using APCI. For cholesterol and cholesterol esters, this results in the same ion ([M-H2O+H]+ @ m/z 369.35) because of source fragmentation. So I get ion clear peak for (free) cholesterol and a minute or two later, when the different cholesterol esters come off, I get wide, complex peak from a lot of (partially) overlapping esters, all visible at m/z 369.35 (see picture below). The first peak gets nicely integrated, the complex one obviously becomes a mess.
What I am trying to do, is to integrate the complex peak as one, so say from 4.7 - 9 min. I figured that could be done by manually change xset@groups[["rtmin"]] and -[["rtmax"]] before doing a fillpeaks. But then, only those samples get reintegrated that missed this peak in the first run. Of course, I can remove all the original integrations from xset@peaks but then I mess up all the idx numbers that are used for grouping in xset@groupidx.
Anyone here who can point me to the right direction? Cheers!
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