As a newcomer to the field, I havent a clue as to how to understand the Adducts column. How is it generated & what does it mean? Is there any general reference for the column headings?
XCMS doesn't calculate the adducts and isotopes. An extension package called CAMERA developed by Steffen Neumanns group takes care of this part of the analysis. The paper is an easy read and highly worth while. There is also the programtic explanation of camera here : http://www.bioconductor.org/packages/re ... CAMERA.pdf (http://www.bioconductor.org/packages/release/bioc/vignettes/CAMERA/inst/doc/CAMERA.pdf)
As for XCMS Online there are some additional steps which are performed to check accuracy of the hits. This area is a hot topic for development and hopefully we will be releasing some new code early next year.
http://www.ncbi.nlm.nih.gov/pubmed/22111785 (http://www.ncbi.nlm.nih.gov/pubmed/22111785)
Anal Chem. 2012 Jan 3;84(1):283-9. doi: 10.1021/ac202450g. Epub 2011 Dec 12.
CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets.
Kuhl C1, Tautenhahn R, Böttcher C, Larson TR, Neumann S.