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A Manual Approach to the CASMI 2014 Challenges and a Review of the Isomer Problem

[ Vol. 5 , Issue. 1 ]


William L. Fitch   Pages 40 - 44 ( 5 )


Background: The CASMI 2014 contest presents challenges in structure determination using mass spectrometry data.

Objective: The contestants solve the problems comparing different software approaches.

Methods: This paper reports a manual approach to structure determination.

Results: The author successfully determined 31/42 molecular formulas and 21/42 structures. Five of the formulas were identified correctly but reported incorrectly. In 4 cases the author identified the wrong ion as the molecular species and so calculated the formula of an adduct or a fragment. In two cases, the author misidentified the formula due to not considering all possible atom combinations. For 6 of the structure misses, the author started with the wrong formula. In 13 cases, the author had the correct formula but reported only one of the possible isomers and these were the wrong isomer. In two cases, no result was reported.

Conclusion: The manual approach is successful at obtaining the correct molecular formula but made it more difficult to generate a list of possible isomers. Suggestions are made for including relative retention, pH effect on retention and H/D exchange information in future CASMI challenges to facilitate isomer identification.


CASMI, dereplication, liquid chromatography, mass spectrometry, metabolomics.


Department of Gastroenterology and Hepatology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305

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