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Metabolites 2013, 3(2), 397-411; doi:10.3390/metabo3020397
Article

CASMI—The Small Molecule Identification Process from a Birmingham Perspective

1
, 1
, 2
, 3
, 1
 and 1,*
1 School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK 2 College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China 3 School of Computer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
* Author to whom correspondence should be addressed.
Received: 1 April 2013 / Revised: 8 May 2013 / Accepted: 10 May 2013 / Published: 21 May 2013
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Abstract

The Critical Assessment of Small Molecule Identification (CASMI) contest was developed to provide a systematic comparative evaluation of strategies applied for the annotation and identification of small molecules. The authors participated in eleven challenges in both category 1 (to deduce a molecular formula) and category 2 (to deduce a molecular structure) related to high resolution LC-MS data. For category 1 challenges, the PUTMEDID_LCMS workflows provided the correct molecular formula in nine challenges; the two incorrect submissions were related to a larger mass error in experimental data than expected or the absence of the correct molecular formula in a reference file applied in the PUTMEDID_LCMS workflows. For category 2 challenges, MetFrag was applied to construct in silico fragmentation data and compare with experimentally-derived MS/MS data. The submissions for three challenges were correct, and for eight challenges, the submissions were not correct; some submissions showed similarity to the correct structures, while others showed no similarity. The low number of correct submissions for category 2 was a result of applying the assumption that all chemicals were derived from biological samples and highlights the importance of knowing the origin of biological or chemical samples studied and the metabolites expected to be present to define the correct chemical space to search in annotation processes.
Keywords: CASMI; metabolite annotation; metabolite identification; KEGG; ChemSpider; PUTMEDID-LCMS; MetFrag CASMI; metabolite annotation; metabolite identification; KEGG; ChemSpider; PUTMEDID-LCMS; MetFrag
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Allwood, J.W.; Weber, R.J.; Zhou, J.; He, S.; Viant, M.R.; Dunn, W.B. CASMI—The Small Molecule Identification Process from a Birmingham Perspective. Metabolites 2013, 3, 397-411.

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