I'm trying to use CAMERA to annotate peaks from data collected in ESI- on a QToF in single-MS mode. I started off using the parameters listed in "LC-MS Peak Identification and Annotation with CAMERA" by Carsten Kuhl, Ralf Tautenhahn and Steffen Neumann, and then, when those parameters gave the result that many, many ions were all caused by the same compound, I tried adjusting. I've tried making my parameters stricter and stricter, and I've now got parameters that suggest that we've got the world's most amazingly mass- and retention-time accurate QToF, but I'm still coming up with the same number of grouped features every time. For example, a bunch of stuff co-elutes around 12.5 minutes, and CAMERA has put 137 ions into that pcgroup, and I just can't believe that one compound could really generate 137 ions. What am I doing wrong? Am I misunderstanding the output? I thought that CAMERA would take a peak-picked, peak-aligned and peak-filled XCMS object and determine which of all those mass features were caused by the same compound. For example, let's say that two compounds co-elute and each generates one Na adduct and one 13C peak in addition to their major, monoisotopic peak. Doesn't CAMERA then decipher those data and tell you, "Hey, it looks like you've got two different compounds that co-elute and these three peaks are because of compound A and those three peaks are because of compound B."? Wouldn't those two compounds have a different number listed under pcgroup?
Here's the code I'm using, in case that's illuminating.
Set1.annot <- xsAnnotate(Set1.filledpeaks)
Set1.F <- groupFWHM(Set1.annot, perfwhm=0.005)
Set1.C <- groupCorr(Set1.F, cor_eic_th=1.6, pval=0.001, calcIso=TRUE,
calcCiS=TRUE)
Set1.FI <- findIsotopes(Set1.C, maxcharge=3, maxiso=4, ppm=10,
mzabs=0.0001, intval="maxo", minfrac=0.1)
Set1.FA <- findAdducts(Set1.FI, ppm=10, mzabs=0.0001, multiplier=3,
polarity="negative", rules=NULL, max_peaks=100)
Set1.peaklist <- getPeaklist(Set1.FA)
write.csv(Set1.peaklist, file="Set1 annotated peaklist.csv")
By the way, what are the allowable numbers for cor_eic_th? Is that referring to equation 1 in Kuhl 20012 Analytical Chemistry? So can that parameter range from 0 to 3?
Thank you very much in advance!
Laura