Identifying unknown metabolites using NMR-based metabolic profiling techniques
File(s)
Accepted version
Author(s)
Garcia Perez, Isabel
Posma, Joram Matthias
Serrano Contreras, Jose Ivan
Boulange, Claire
Chan, Queenie
Type
Journal Article
Abstract
Metabolic profiling of biological samples provides important insights into multiple physiological and pathological processes, but is hindered by a lack of automated annotation and standardised methods for structure elucidation of candidate disease biomarkers. Here, we describe a system for identifying molecular species derived from NMR spectroscopy based metabolic phenotyping studies, with detailed info on sample preparation, data acquisition, and data modelling. We provide eight different modular workflows to be followed in a recommended sequential order according to their level of difficulty. This multi-platform system involves the use of statistical spectroscopic tools such as STOCSY, STORM and RED-STORM to identify other signals in the NMR spectra relating to the same molecule. It also utilizes 2D-NMR spectroscopic analysis, separation and pre-concentration techniques, multiple hyphenated analytical platforms and data extraction from existing databases. The complete system, using all eight workflows, would take up to a month, as it includes multidimensional NMR experiments that require prolonged experiment times. However, easier identification cases using fewer steps would take two or three days. This approach to biomarker discovery is efficient, cost-effective and offers increased chemical space coverage of the metabolome, resulting in faster and more accurate assignment of NMR-generated biomarkers arising from metabolic phenotyping studies. Finally, it requires basic understanding of Matlab in order to perform statistical spectroscopic tools and analytical skills to perform Solid Phase Extraction, LC-fraction collection, LC-NMR-MS and 1D and 2D NMR experiments.
Date Issued
2020-08-01
Date Acceptance
2020-05-04
Citation
Nature Protocols, 2020, 15, pp.2538-2567
ISSN
1750-2799
Publisher
Nature Research
Start Page
2538
End Page
2567
Journal / Book Title
Nature Protocols
Volume
15
Copyright Statement
© 2020 Springer Nature Limited.
Sponsor
Medical Research Council (MRC)
Medical Research Council
National Institute for Health Research
National Institutes of Health
National Institute for Health Research
Medical Research Council (MRC)
UK DRI Ltd
National Institute for Health Research
Grant Number
MR/S004033/1
MR/S004033/1
NIHR-CDF-2017-10-023
IMTERMAP Subaward No. 60024563
NF-SI-0513-10029
MR/S019669/1
4050641385
NF-SI-0508-10112
Subjects
Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Biochemistry & Molecular Biology
NUCLEAR-MAGNETIC-RESONANCE
TOTAL CORRELATION SPECTROSCOPY
MHZ H-1-NMR SPECTROSCOPY
ANGLE-SPINNING NMR
2-DIMENSIONAL SPECTROSCOPY
INFORMATION RECOVERY
BIOMARKER DISCOVERY
BIOLOGICAL-FLUIDS
DRUG-METABOLISM
BLOOD-PLASMA
Bioinformatics
03 Chemical Sciences
06 Biological Sciences
11 Medical and Health Sciences
Publication Status
Published
Date Publish Online
2020-07-17