Birmingham Metabolite Library: a publicly accessible database of 1-D 1H and 2-D 1H J-resolved NMR spectra of authentic metabolite standards (BML-NMR)

Abstract

Public databases of NMR spectra of low molecular weight metabolites must be constructed to remove the major bottleneck of metabolite identification and quantification in the analysis of metabolomics data. Two-dimensional (2-D) 1 H J-resolved spectroscopy represents a popular alternative to 1-D NMR methods, resolving the highly overlapped signals characteristic of complex metabolite mixtures across two frequency dimensions. Here we report the design, measurement and curation of, primarily, a database of 2-D J-resolved NMR spectra.Metabolites were selected based upon their importance within metabolic pathways and their detection potential by NMR, and prepared for analysis at pH 6.6, 7.0 and 7.4. Sixteen NMR spectra were recorded for each metabolite using a 500 MHz spectrometer, including 1-D and 2-D J-resolved spectra, different water suppression methods and different acquisition parameters. Some metabolites were removed due to limited solubility, poor NMR signal quality or contamination, and the final dataset comprised of 3328 NMR spectra arising from 208 metabolite standards. These data are housed in a purpose-built MySQL database (Birmingham Metabolite Library; BML-NMR) containing over 100 separate tables and allowing the efficient storage of raw free-induction-decays (FIDs), 1-D and 2-D NMR spectra and associated metadata. The database is compliant with the Metabolomics Standards Initiative (MSI) endorsed reporting requirements, with some necessary amendments. Library data can be accessed freely and searched through a custom written web interface (www.bml-nmr.org). FIDs, NMR spectra and associated metadata can be downloaded according to a newly implemented MSI-compatible XML schema.

Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D 1H-NMR data

“…This characteristic subset of spectral resonances is stored in a proprietary library edited specifically for the kind of sample under study. The metabolite information about peak positions, signal multiplicity, and J-coupling values is included in the library, and is based on public domain databases such as the Human Metabolome Database (HMDB) [28], the Birmingham Metabolite Library [29], and the BioMagResBank (BMRB) [30], or commercial packages such as Chenomx NMR Suite (Chenomx Inc., Edmonton, Alberta, Canada) and Bioref Amix (Bruker, GmbH, Silberstreifen, Rheinstetten, Germany).…”

Databases and Software for NMR-Based Metabolomics

“…The Birmingham Metabolite Library (BML-NMR) [11] offers standard spectra collected under two types of water suppression, multiple excitation angles, multiple interscan relaxation delays and a range of pH values (6.6, 7.0 and 7.4). The use of multiple interscan relaxation delays is particularly useful for quantitative NMR in that it may provide a basis for estimating T 1 values.…”

Probing Cancer Cell Metabolism Using NMR Spectroscopy

“…This is not possible using a 1D 1 H NMR spectroscopic approach. Metabolites in 2D-Jres spectra can still be quantifi ed using spectral databases [ 33 ].…”