The XCMS16 Bioconductor package32 is the most widely used software for processing untargeted LC-MS-based metabolomics data. Its results can be further processed with the CAMERA13 package to determine which of the extracted m/z-rt features might be adducts13 or isotopes33 of the same original compound. For the integration of XCMS and CAMERA into the IIMN workflow, utility functions were created (‘getFeatureAnnotations‘ and ‘getEdgelist‘) to extract and export MS1 based feature and edge annotations (i.e., grouping of features to adduct/isotope groups of the same compound). In addition, the utility function ‘formatSpectraForGNPS‘ is used to export MS2 spectra. These functions are available in the GitHub repository https://github.com/jorainer/xcms-gnps-tools. R-markdown documents and python scripts with example analyses and descriptions are available in the documentation. (https://ccms-ucsd.github.io/GNPSDocumentation/fbmn-iin-xcms/) The files exported by these utility functions can be directly used for IIMN analysis on GNPS. Note that theoretically, it is possible to use RAMClust10, CliqueMS14, or other packages available for XCMS that perform ion annotation. The results of these packages need to be reformatted to the introduced generic supplementary edges format. The CAMERA integration might serve as a reference and starting point.

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