The impact of the method of extracting metabolic signal from 1H-NMR data on the classification of samples: A case study of binning and BATMAN in lung cancer

• Published in: PloS one 2019, Vol.14 (2), p.e0211854-e0211854
• Main Authors: Padayachee, Trishanta, Khamiakova, Tatsiana, Louis, Evelyne, Adriaensens, Peter, Burzykowski, Tomasz
• Format: Article
• Language: English
• Subjects: Adult; Algorithms; Bayes Theorem; Bayesian analysis; Biological samples; Biology and Life Sciences; Blood plasma; Cancer; Case reports; Case studies; Chemical composition; Chemical equilibrium; Classification; Data processing; Deconvolution; Discriminant analysis; Engineering and Technology; Female; Humans; Hydrogen; Integration; Lung cancer; Lung diseases; Lung Neoplasms - blood; Magnetic fields; Magnetic resonance; Male; Mathematical models; Medicine and Health Sciences; Metabolism; Metabolites; Metabolome; Metabolomics; Methods; NMR; Nuclear magnetic resonance; Nuclear Magnetic Resonance, Biomolecular; Organic chemistry; Patients; Physical Sciences; R&D; Research & development; Research and analysis methods; Resonance; Signal Processing, Computer-Assisted; Software; Spectra; Spectral signatures; Spectroscopy; Statistical analysis; Statistical methods
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0211854

Nuclear magnetic resonance (NMR) spectroscopy is a principal analytical technique in metabolomics. Extracting metabolic information from NMR spectra is complex due to the fact that an immense amount of detail on the chemical composition of a biological sample is expressed through a single spectrum. The simplest approach to quantify the signal is through spectral binning which involves subdividing the spectra into regions along the chemical shift axis and integrating the peaks within each region. However, due to overlapping resonance signals, the integration values do not always correspond to the concentrations of specific metabolites. An alternate, more advanced statistical approach is spectral deconvolution. BATMAN (Bayesian AuTomated Metabolite Analyser for NMR data) performs spectral deconvolution using prior information on the spectral signatures of metabolites. In this way, BATMAN estimates relative metabolic concentrations. In this study, both spectral binning and spectral deconvolution using BATMAN were applied to 400 MHz and 900 MHz NMR spectra of blood plasma samples from lung cancer patients and control subjects. The relative concentrations estimated by BATMAN were compared with the binning integration values in terms of their ability to discriminate between lung cancer patients and controls. For the 400 MHz data, the spectral binning approach provided greater discriminatory power. However, for the 900 MHz data, the relative metabolic concentrations obtained by using BATMAN provided greater predictive power. While spectral binning is computationally advantageous and less laborious, complementary models developed using BATMAN-estimated features can add complementary information regarding the biological interpretation of the data and therefore are clinically useful.