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

Full Text: gku436.pdf PDF

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.

Citation

F. Allen, A. Pon, M. Wilson, R. Greiner, D. Wishart. "CFM-ID: A web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra". Nucleic Acids Research (NAR), 42(W1), pp W94-W99, July 2014.

Keywords: bioinformatics, metabolomics, mass spec, metabolite identification
Category: In Journal
Web Links: Journal URL
  DOI

BibTeX

@article{Allen+al:NAR14,
  author = {Felicity Allen and Allison Pon and Michael Wilson and Russ Greiner
    and David S. Wishart},
  title = {CFM-ID: A web server for annotation, spectrum prediction and
    metabolite identification from tandem mass spectra},
  Volume = "42",
  Number = "W1",
  Pages = {W94-W99},
  journal = {Nucleic Acids Research (NAR)},
  year = 2014,
}

Last Updated: March 10, 2020
Submitted by Sabina P

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