More information on the Competitive Fragmentation Modeling method and this web server can be found in the following publications:
Djoumbou-Feunang Y, Pon A, Karu N, Zheng J, Li C, Arndt D, Gautam M, Allen F, and Wishart D. Significantly Improved ESI-MS/MS Prediction and Compound Identification. Metabolites. April 13, 2019, 9(4), 72.
Allen F, Greiner R, and Wishart D. Computational prediction of electron ionization mass spectra to assist in GC-MS compound identification. Anal. Chem. July 6, 2016, 88(15), 7689–7697.
Supporting Data: https://sourceforge.net/p/cfm-id/code/HEAD/tree/supplementary_material/2016_ei_ms_paper/
Allen F, Greiner R, and Wishart D. Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics. June 2014.
Supporting Data: https://sourceforge.net/p/cfm-id/code/HEAD/tree/supplementary_material/2015_esi_msms_paper/
Allen F, Pon A, Wilson M, Greiner R, and Wishart D. CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res. June 2014.
Source code for the rule-based fragmentation tool is available at https://bitbucket.org/wishartlab/msrb-fragmenter. Windows executables and cross-platform source code for the combinatorial fragmentation tool are freely available at http://sourceforge.net/projects/cfm-id. Supplementary files containing test molecule lists and trained models are also available on that site.