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?
Well it clearly depends on the capability of the tools, probably your question can be more likely be answered in a Mass-Spec forum or at the (Github) pages of the packages.
Are you looking for an universal solution or for something that matches your datasets?
Even when they used a certain method as showcase it doesn't mean it's not working with another one.
The LC shouldn't make a difference. In any case you should be able to identify the compounds with their retention time and m/z. However it could be possible, that some peak-integration defaults are hardcoded in the tool that simply do not work with all possible separation types. In a perfect world you can adjust this - as far as I know XCMS offers a lot of flexibility.
The MS however can make a difference, just because the data look different if you just have MS or MS/MS. In the latter case you have more dimensions, not every software might be designed to work with this.