CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W94-9. doi: 10.1093/nar/gku436. Epub 2014 Jun 3.


CFM-ID is a web server supporting three tasks associated with the interpretation of tandem mass spectra (MS/MS) for the purpose of automated metabolite identification: annotation of the peaks in a spectrum for a known chemical structure; prediction of spectra for a given chemical structure and putative metabolite identification--a predicted ranking of possible candidate structures for a target spectrum. The algorithms used for these tasks are based on Competitive Fragmentation Modeling (CFM), a recently introduced probabilistic generative model for the MS/MS fragmentation process that uses machine learning techniques to learn its parameters from data. These algorithms have been extensively tested on multiple datasets and have been shown to out-perform existing methods such as MetFrag and FingerId. This web server provides a simple interface for using these algorithms and a graphical display of the resulting annotations, spectra and structures. CFM-ID is made freely available at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Artificial Intelligence
  • Humans
  • Internet
  • Metabolomics / methods*
  • Models, Statistical
  • Software*
  • Tandem Mass Spectrometry / methods*