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Topic: How to extract parent ion? (Read 2171 times) previous topic - next topic

How to extract parent ion?

Dear XCMS-CAMERA community,
I hope to use CAMERA to shorten my LC-MS feature list to a list with parent ions only. I followed the CAMERA annotation and identification workflow described for multiple samples (1). Using the wrapper function annotateDiffreport, I got a list with columns for isotopes, adducts and pcgroups.
But I don’t understand how to extract the parent ions from the pcgroups. I figured, there probably is a function for that?
Sometimes a peakgroup contains a lot of different features with a lot of different potential parent ions. How do I deal with a group like that?
I was also wondering, if the algorithm of the xcms online tool for the annotation of isotopes and adducts is related to the one used in CAMERA?
I am new to metabolite analysis and R and I am happy to provide further information if needed.
I greatly appreciate your help!
Thank you very much!

Nadine

(1) http://https://bioconductor.org/packages/release/bioc/vignettes/CAMERA/inst/doc/CAMERA.pdf