Dear marmian, I am very new to msdial so my advise may not be the best but I experienced similar issues. For me, what worked was to extrart the downloaded .zip file in a "\temp\" directory and run msdial.exe as an administrator. Possibly something to do with writing rights?
I need a small peakwidth because of triacylglycerols coming off around the same time as the cholesterol esters. Isobaric compounds (different combinations acyl chains that add up to the same m/z but are chromatographically separated) that elute close together. Everything is fine, except the CholE.
However, explaining the problem here, led me to a solution: what I needed was getPeaks(). One can define the peakrange (an mz range and rt range) and get the integrated peak area from the xcmsRaw object. I will replace the appropriate xset@peaks with the result from this function and that should do the trick.
I was thinking to change the rt boundaries in xset@groups, clearing out the xset@groupidx and then do a fillpeaks, leaving the original peaks intact to prevent messing up the peakidx part. But feeding an empty list to fillpeaks() doesn't seem to be allowed.
I'm running into a problem that must have been solved a million times but I just cannot find a solution.
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!