I am reviewing the R packages/libraries to do LC MS processing and analysis. So far I found the xcms and MITE packages. As I read the tutorials, I find that there are different chromatography and mass spec methods and I wonder if there are specific packages matching the different chromatography and ms methods. For example HPLC or reverse phase HPLC for chromatography, or LC MS and LC MS MS.
Could you please point me into the right direction? In other words, do R LC/MS processing and analysis methods dependent on the way the data was obtained? How do I go about selecting the right LC/MS processing and analysis R package?