Metabolite annotation aims to collect and integrate as much information as possible from a given metabolite peak to provide information as to its identity and structure. Although there is no consensus as to the total number of tomato metabolites, 73 and 555 metabolites are registered in the categories Lycopersicon and Solanum, respectively, in the metabolite database Dictionary of Natural Products (http://www.chemnetbase.com/ scripts/dnpweb.exe?welcome-main) as of March 2007. In two separate studies, 92 and 110 metabolites were found in tomato fruit by GC-MS and LC-Q-TOF-MS, respectively (Carrari etal. 2006; Moco et al. 2006). It has been reported that approximately 11,500 ions were detected from red tomato fruit extract by LC-Q-TOF-MS (Bino et al. 2005), which raises the possibility that the number of published tomato metabolites has not come close to approaching the total number. Many unknown metabolites await identification; this has been a major constraint in plant metabolomics due to the lack of standard chemicals corresponding to myriads of secondary metabolites. One solution is to develop a methodology to discriminate each unknown peak by providing a series of "annotations". An operational definition of metabolite annotation is to cluster detected peaks into peak groups that represent individual metabolites, and to provide chemical information concerning the peak groups, including m/z value, MS/MS fragmentation pattern, UV/visible absorption spectrum, retention time, putative molecular formula, putative structure predicted from MS/MS fragmentation patterns, and search results of databases and scientific literature. An annotation is useful for two aspects of biological analyses. First, it allows consistent identification of unknown peaks across a number of samples by using a combination of chemical data obtained for the peak. Second, a combination of m/z value and MS/MS fragmentation pattern provides critical information for predicting the molecular structure of the metabolite. MS/MS fragmentation patterns allow prediction of metabolite component moieties without elucidating metabolite stereo-structure. An annotation obtained by this procedure may serve as the primary, or mass spectral, annotation. A secondary, or biological annotation of a metabolite describes the tissues and environmental conditions under which a given metabolite was found. Concepts of metabolite annotation have been reviewed by Kind and Fiehn (2006) and Fiehn et al. (2005).
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