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

CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Allen, F., Wilson, M., Pon, A., Greiner, R., & Wishart, D. Nucleic Acids Res, 42(W1):W94-W99, 2014.
doi abstract bibtex

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 http://cfmid.wishartlab.com.

@Article{allen14cfm-id,
  author    = {Felicity Allen and Michael Wilson and Allison Pon and Russ Greiner and David Wishart},
  journal   = {Nucleic Acids Res},
  title     = {{CFM-ID:} A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra},
  year      = {2014},
  number    = {W1},
  pages     = {W94-W99},
  volume    = {42},
  abstract  = {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 http://cfmid.wishartlab.com.},
  doi       = {10.1093/nar/gku436},
  file      = {AllenEtAl_CFMIDWebServer_NuclAcidsRes_2014.pdf:2014/AllenEtAl_CFMIDWebServer_NuclAcidsRes_2014.pdf:PDF},
  keywords  = {MS; metabolite identification; CFM; CFM-ID;},
  owner     = {kaidu},
  timestamp = {2014.05.06},
}

Downloads: 0

{"_id":"dcYnuNHGagbMY3ENr","bibbaseid":"allen-wilson-pon-greiner-wishart-cfmidawebserverforannotationspectrumpredictionandmetaboliteidentificationfromtandemmassspectra-2014","authorIDs":[],"author_short":["Allen, F.","Wilson, M.","Pon, A.","Greiner, R.","Wishart, D."],"bibdata":{"bibtype":"article","type":"article","author":[{"firstnames":["Felicity"],"propositions":[],"lastnames":["Allen"],"suffixes":[]},{"firstnames":["Michael"],"propositions":[],"lastnames":["Wilson"],"suffixes":[]},{"firstnames":["Allison"],"propositions":[],"lastnames":["Pon"],"suffixes":[]},{"firstnames":["Russ"],"propositions":[],"lastnames":["Greiner"],"suffixes":[]},{"firstnames":["David"],"propositions":[],"lastnames":["Wishart"],"suffixes":[]}],"journal":"Nucleic Acids Res","title":"CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra","year":"2014","number":"W1","pages":"W94-W99","volume":"42","abstract":"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 http://cfmid.wishartlab.com.","doi":"10.1093/nar/gku436","file":"AllenEtAl_CFMIDWebServer_NuclAcidsRes_2014.pdf:2014/AllenEtAl_CFMIDWebServer_NuclAcidsRes_2014.pdf:PDF","keywords":"MS; metabolite identification; CFM; CFM-ID;","owner":"kaidu","timestamp":"2014.05.06","bibtex":"@Article{allen14cfm-id,\n author = {Felicity Allen and Michael Wilson and Allison Pon and Russ Greiner and David Wishart},\n journal = {Nucleic Acids Res},\n title = {{CFM-ID:} A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra},\n year = {2014},\n number = {W1},\n pages = {W94-W99},\n volume = {42},\n abstract = {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 http://cfmid.wishartlab.com.},\n doi = {10.1093/nar/gku436},\n file = {AllenEtAl_CFMIDWebServer_NuclAcidsRes_2014.pdf:2014/AllenEtAl_CFMIDWebServer_NuclAcidsRes_2014.pdf:PDF},\n keywords = {MS; metabolite identification; CFM; CFM-ID;},\n owner = {kaidu},\n timestamp = {2014.05.06},\n}\n\n","author_short":["Allen, F.","Wilson, M.","Pon, A.","Greiner, R.","Wishart, D."],"key":"allen14cfm-id","id":"allen14cfm-id","bibbaseid":"allen-wilson-pon-greiner-wishart-cfmidawebserverforannotationspectrumpredictionandmetaboliteidentificationfromtandemmassspectra-2014","role":"author","urls":{},"keyword":["MS; metabolite identification; CFM; CFM-ID;"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://git.bio.informatik.uni-jena.de/fleisch/literature/raw/master/group-literature.bib","creationDate":"2019-11-19T16:50:41.441Z","downloads":0,"keywords":["ms; metabolite identification; cfm; cfm-id;"],"search_terms":["cfm","web","server","annotation","spectrum","prediction","metabolite","identification","tandem","mass","spectra","allen","wilson","pon","greiner","wishart"],"title":"CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra","year":2014,"dataSources":["C5FtkvWWggFfMJTFX"]}