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XCMS / Beginner to MS, how to pick parameters?
I have no idea or how to evaluate if my parameters were good. I was wondering if anyone could recommend parameters for a UPLC LC-MS run done on Bruker maXis impact in positive mode. The run was 22 minutes long, and m/z scan range was 50-2000. I basically have been trying to assess what kind of peak width parameter to use, profStep for grouping, and furthermore how to evaluate if the features detected are reliable and of best quality(?). My ultimate goal is to create an excel like document (csv or tab delimited) of the m/z ions detected, the retention time, and the intensity of that ion detected throughout my samples. Is something like this possible with XCMS?
I'm sorry if this question is incredibly basic, but I am having a hard time getting started and I have no idea how to evaluate my results from XCMS. Here is previous parameters I have used:
xset_cent20 <- xcmsSet(files,method="centWave", ppm=20, snthr=10,peakwidth=c(5,25), integrate = 2)
xset_cent20g<- group(xset_cent20)
xset_cor20<- retcor(xset_cent20g)