%0 Journal Article
%T Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm
%A Tobias Kind
%A Oliver Fiehn
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-234
%X High mass accuracy (<1 ppm) alone is not enough to exclude enough candidates with complex elemental compositions (C, H, N, S, O, P, and potentially F, Cl, Br and Si). Use of isotopic abundance patterns as a single further constraint removes >95% of false candidates. This orthogonal filter can condense several thousand candidates down to only a small number of molecular formulas. Example calculations for 10, 5, 3, 1 and 0.1 ppm mass accuracy are given. Corresponding software scripts can be downloaded from http://fiehnlab.ucdavis.edu webcite. A comparison of eight chemical databases revealed that PubChem and the Dictionary of Natural Products can be recommended for automatic queries using molecular formulae.More than 1.6 million molecular formulae in the range 0¨C500 Da were generated in an exhaustive manner under strict observation of mathematical and chemical rules. Assuming that ion species are fully resolved (either by chromatography or by high resolution mass spectrometry), we conclude that a mass spectrometer capable of 3 ppm mass accuracy and 2% error for isotopic abundance patterns outperforms mass spectrometers with less than 1 ppm mass accuracy or even hypothetical mass spectrometers with 0.1 ppm mass accuracy that do not include isotope information in the calculation of molecular formulae.Metabolomics seeks to identify and quantify all metabolites in a given biological context [1]. In this respect its aim is different from metabolic fingerprinting or metabonomic approaches which utilize high dimensional unannotated variables and multivariate statistics to find biomarkers that may or may not be structurally identified in subsequent steps. Therefore, an important task in metabolomics is to identify or structurally annotate compounds in a high throughput manner. Mass spectrometry is one of the most powerful tools for unbiased analysis of small molecules in life sciences. Hundreds to thousands of metabolites can be detected when suitable sample preparation metho
%U http://www.biomedcentral.com/1471-2105/7/234