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.