title: CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra.
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.
authors.affiliation: Department of Computing Science, Athabasca Hall, University of Alberta, Edmonton T6G 2E8, Canada. felicity.allen@ualberta.ca.
authors.forename: Felicity
authors.initials: F
authors.lastname: Allen
authors.affiliation: Department of Computing Science, Athabasca Hall, University of Alberta, Edmonton T6G 2E8, Canada.
authors.forename: Allison
authors.initials: A
authors.lastname: Pon
authors.affiliation: Department of Computing Science, Athabasca Hall, University of Alberta, Edmonton T6G 2E8, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Wilson
authors.affiliation: Department of Computing Science, Athabasca Hall, University of Alberta, Edmonton T6G 2E8, Canada.
authors.forename: Russ
authors.initials: R
authors.lastname: Greiner
authors.affiliation: Department of Computing Science, Athabasca Hall, University of Alberta, Edmonton T6G 2E8, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Wishart
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D006801:Humans; D020407:Internet; D055432:Metabolomics / Q000379:methods*; D015233:Models, Statistical; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*