After finding isotopes, is it possible to pick an isotope group and plot the EICs just from that isotope group for a specific sample? I don't want to plot an entire peak group; I would like to see just the EICs for all the ions that CAMERA has assigned to the same isotope group. I thought maybe getIsotopeCluster would be a step in the right direction, but I don't know what to do after that.
On that topic, when getIsotopeCluster or any of the other commands in CAMERA ask for "value" or "intval", what do "maxo", "into" and "intb" refer to?
Thanks!
Laura
Hi Laura,
good question, because the output of getIsotopeCluster can't be mapped directly.
It would be a larger code snippet, so I prefer a small change in the function itself.
I report back, as soon as I'm finished.
Concerning the value argument:
xcms reports 3 different intensity values for each peak.
maxo - maximum peak intensity
into - integrated peak intensity
intb - integrated peak intensity (baseline corrected)
The choose of the intensity is important for the detection in findIsotopes (for calculation C12/C13 threshold)
Within getIsotopeCluster it only changes the reported intensity value.
Within our data sets the intb values works best, mainly with low peak intensity.
Best,
Carsten