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CFM-ID Applied to CASMI 2014

[ Vol. 5 , Issue. 1 ]


Felicity Allen, Russell Greiner and David Wishart   Pages 35 - 39 ( 5 )


We describe our winning submission to the Critical Assessment of Small Molecule Identification (CASMI) 2014 competition, based on our method called Competitive Fragmentation Modeling (CFM-ID).

Background: The CASMI competition is an annual international competition in which contestants must provide putative chemical structures for each of a set of challenge mass spectra.

Methods: For each target spectrum, we used CFM-ID to provide a score for each candidate compound, based on its ESI-MS/MS spectrum. We combined this with two other scoring components that made use of additional meta information provided with each challenge. We also investigated the role of this meta information in the results obtained.

Results: The resulting method correctly identified 24 out of 42 challenge compounds, and ranked the correct candidate in the top 10 in 33 challenges. The use of the meta information was found to play a significant role in the identification performance.

Conclusion: This was sufficient to win the CASMI competition, which is evolving to become an important arena for assessment of progress in this field.


CASMI contest, MAGMa software, metabolite identification, tandem mass spectrometry, mass fragmentation.


Department of Computing Sceince, 2-21 Athabasca Hall, University of Alberta, Edmonton, T6G 2E8

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