MetAssimulo: simulation of realistic NMR metabolic profiles

• Published in: BMC bioinformatics Vol. 11; no. 1; p. 496
• Main Authors: Muncey, Harriet J, Jones, Rebecca, De Iorio, Maria, Ebbels, Timothy M D
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 06.10.2010; BioMed Central; BMC
• Subjects: Algorithms; Databases, Factual; Magnetic Resonance Spectroscopy - methods; Metabolites; Metabolome; Metabolomics - methods; Metabonomic analysis; Methods; Molecular simulation; NMR; Nuclear magnetic resonance; Software; Spectrum analysis; Studies
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-11-496

Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields highly complex profiles that require sophisticated statistical analysis methods. However, experimental data is difficult to control and expensive to obtain. Thus data simulation is a productive route to aid algorithm development. MetAssimulo is a MATLAB-based package that has been developed to simulate 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database, MetAssimulo is able to create realistic metabolic profiles containing large numbers of metabolites with a range of user-defined properties. Current features include the simulation of two groups ('case' and 'control') specified by means and standard deviations of concentrations for each metabolite. The software enables addition of spectral noise with a realistic autocorrelation structure at user controllable levels. A crucial feature of the algorithm is its ability to simulate both intra- and inter-metabolite correlations, the analysis of which is fundamental to many techniques in the field. Further, MetAssimulo is able to simulate shifts in NMR peak positions that result from matrix effects such as pH differences which are often observed in metabolic NMR spectra and pose serious challenges for statistical algorithms. No other software is currently able to simulate NMR metabolic profiles with such complexity and flexibility. This paper describes the algorithm behind MetAssimulo and demonstrates how it can be used to simulate realistic NMR metabolic profiles with which to develop and test new data analysis techniques. MetAssimulo is freely available for academic use at http://cisbic.bioinformatics.ic.ac.uk/metassimulo/.