My problem is that the features identified by XCMS are off with around 0.02Da compared to raw files (.d) accessed by Bruker's Data Analysis 4.2.
What could be the explanation for this?
I am using RStudio (Version 0.98.994), XCMS (version 1.38.0).
I have a HPLC-qTOF (Bruker) which produces .d files. I have converted these files into .mzXML files by CompassXport 3.0.
Following I run library(xcms)
xset <- xcmsSet(myDir, ppm = 30, peakwidth = c(10,60), method = "centWave", snthresh = 10, noise=100, prefilter = c(4,1000),
mzCenterFun = "wMean", integrate = 1, mzdiff=-0.01, fitgauss = TRUE, profparam = list("step" = 0.01))
xset1 <- group(xset, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset2 <- retcor(xset1, missing = 1, extra = 1, smooth = "loess", span = 0.2, family = "symmetric")
xset3 <- group(xset2, bw = 30, minfrac = 0.5, minsamp = 1, mzwid = 0.025, max = 50)
xset4 <- fillPeaks.chrom(xset3)
reporttab <- diffreport(xset4, "A", "B", "Outputfile2", 11, metlin = 0.15, h = 480, w = 640)
xset5 <- peakTable(xset4, filebase="name")
Any help is really appreciated!