Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications

• Published in: Bioinformatics (Oxford, England) England), 2011-02, Vol.27 (4), p.524-533
• Main Authors: SCHLEIF, F.-M, RIEMER, T, BÖRNER, U, SCHNAPKA-HILLE, L, CROSS, M
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acids - chemistry; Animals; Biological and medical sciences; Cell Line; Fittings; Fundamental and applied biological sciences. Psychology; General aspects; Genetic algorithms; Least-Squares Analysis; Magnetic Resonance Imaging; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Metabolites; Mice; Nuclear magnetic resonance; Profiling; Signatures; Spectra; Stem Cells - chemistry; Systems Biology - methods; Uncertainty
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btq661

The analysis of metabolic processes is becoming increasingly important to our understanding of complex biological systems and disease states. Nuclear magnetic resonance spectroscopy (NMR) is a particularly relevant technology in this respect, since the NMR signals provide a quantitative measure of the metabolite concentrations. However, due to the complexity of the spectra typical of biological samples, the demands of clinical and high-throughput analysis will only be fully met by a system capable of reliable, automatic processing of the spectra. An initial step in this direction has been taken by Targeted Profiling (TP), employing a set of known and predicted metabolite signatures fitted against the signal. However, an accurate fitting procedure for (1)H NMR data is complicated by shift uncertainties in the peak systems caused by measurement imperfections. These uncertainties have a large impact on the accuracy of identification and quantification and currently require compensation by very time consuming manual interactions. Here, we present an approach, termed Extended Targeted Profiling (ETP), that estimates shift uncertainties based on a genetic algorithm (GA) combined with a least squares optimization (LSQO). The estimated shifts are used to correct the known metabolite signatures leading to significantly improved identification and quantification. In this way, use of the automated system significantly reduces the effort normally associated with manual processing and paves the way for reliable, high-throughput analysis of complex NMR spectra. The results indicate that using simultaneous shift uncertainty correction and least squares fitting significantly improves the identification and quantification results for (1)H NMR data in comparison to the standard targeted profiling approach and compares favorably with the results obtained by manual expert analysis. Preservation of the functional structure of the NMR spectra makes this approach more realistic than simple binning strategies.