Abstract: Metabolomics involves the rapid, high throughput characterization of the small molecule me

1
NMR and the Human Metabolome Project David S.
Wishart, Brian D. Sykes, Hans Vogel, Derrick
Clive, Liang Li, Russ Greiner, Mike Ellison and
Fiona Bamforth University of Alberta, Edmonton,
AB, Canada T6G 2E8
Abstract Metabolomics involves the rapid, high
throughput characterization of the small molecule
metabolites found in an organism. NMR
spectroscopy is promising to play an increasingly
important role in metabolomics. Since the
metabolome is closely tied to the genotype of an
organism, its physiology and its environment,
metabolomics offers a unique opportunity to look
at genotype-phenotype as well as
genotype-envirotype relationships. Metabolomics
is increasingly being used in a variety of health
applications including pharmacology, pre-clinical
drug trials, toxicology, transplant monitoring,
newborn screening and clinical chemistry.
However, a key limitation to metabolomics is the
fact that the human metabolome is not at all well
characterized. Unlike the situation in genomics,
where the human genome is now fully sequenced and
freely accessible, metabolomics is not nearly as
developed. It is estimated that only ¼ to ½ of
endogenous human metabolites in blood or urine
have been positively identified. Of those that
have been identified, very few have any
information on their normal concentration ranges.
Further, there is no publicly available,
electronic database for human metabolites (i.e.
no Metabo-Bank) and there are no metabolite
libraries which allow researcher to obtain
quantities of rare metabolites from which to
standardize their instruments. To address these
issues we have initiated the Human Metabolome
Project, with the aim of completing the human
metabolome by 2007. This will involve
identifying, spectroscopically characterizing
(via NMR), and quantifying an estimated 1400
endogenous metabolites that can be found in
urine, blood, CSF and white blood cells at
concentrations greater than 1 micromolar. This
project will combine high throughput NMR methods
along with FT-MS and other analytical techniques
to identify and quantify metabolite and their
concentration ranges from a large number of human
samples. The data and the compounds isolated,
synthesized or purchased from this project will
be used to create a freely available electronic
database called the human metabolite database
(HMDB) and a commercial chemical warehouse
called the human metabolite library (HML) with
mg-gram quantities of these metabolites. I will
describe the status of the human metabolome
project, the HMD and HML as well as some
interesting health and health research
applications that make use of NMR in metabolic
profiling.
Introduction
The Role of NMR
The HMDB
The metabolome is defined as the complete set of
endogenous small molecule metabolites found in an
organism. Since the metabolome is closely tied
to an organisms genotype, its physiology and its
environment (what the organism eats or breathes),
metabolomics offers a unique opportunity to look
at genotype-phenotype as well as
genotype-environment relationships. Metabolomics
is increasingly being used in a variety of health
applications including pharmacology, pre-clinical
drug trials, toxicology, transplant monitoring,
newborn screening and clinical chemistry.
However, a key limitation to metabolomics is the
fact that the human metabolome is not at all well
characterized.
Over the next 2.5 years we expect to compile
detailed data (spectra, phys-chem parameters, and
concentration data) on most kinds of human
metabolites. Already we have compiled data on
729 metabolites and placed them into a first
draft of an on-line human metabolite database
(HMDB). It is available at http//www.hmdb.ca To
date 212 chemical compounds have been purchased
or acquired and another 420 have been identified
as the next to be acquired, synthesized or
isolated. Approximately 100 new compounds are
added to the database every month.
NMR will play a critical role in just about every
aspect of the Human Metabolome Project. NMR will
be used to formally characterize and assess all
compounds purchased, synthesized or isolated
during the lifetime of this project. Complete
sets of 1H and 13C spectra (500-800 MHz) will be
collected and made available for all compounds in
the HMDB. NMR will also be used to identify new
compounds and to quantify the concentrations of
many compounds in various biofluids
project we are working towards completing the
human metabolome. This will involve identifying
and quantifying an estimated 1400 endogenous
metabolites that can be found in urine, blood,
CSF and white blood cells at concentrations
greater than 1 micromolar. The data and the
compounds isolated, synthesized or purchased from
this work will be used to create a freely
available electronic database called the human
metabolite database (HMDB) and an open access
warehouse of chemicals called the human
metabolite library (HML).
Project Participants
The Human Metabolome Project brings together 8
PIs from a broad variety of backgrounds
including clinical chemistry, biochemistry,
analytical chemistry, organic chemistry
computing science. It is expected that another 20
individuals will be hired to work on various
aspects of the project. We are hiring now!
Metabolomics Proteomics Genomics
1400?? Chemicals
Once the Human Metabolome Project is complete,
NMR will also play a crucial role in rapidly
identifying and quantifying metabolites via
metabolic profiling experiments. Companies such
as Chenomx, Metabometrix, Varian and Bruker will
use NMR spectra of pure compounds to rapidly (lt
30 s) deconvolute the spectra of biofluid mixtures
3000 Enzymes
30,000 Genes
Brian Sykes Biochemistry U of Alberta NMR spect.
Russ Greiner Comp. Sci. U of Alberta Bioinformatic
s
David Wishart Comp. Sci. U of Alberta Proj. Leader
Hans Vogel Biochemistry U of Calgary NMR spect.
Figure 1. The Pyramid of Life, a diagram
illustrating the relationship between
metabolomics, genomics and proteomics.
A Modest Proposal
Figure 1. Screen shot montage of the Human
Metabolome Database web pages. These shots show
examples of the browser/sorter (top), the
metabocard for each metabolite (50 fields of
data left), the structure viewing applet
(right) and the structure query tool to allow
individuals to search by structure similarity
(bottom). All metabolites will be linked to
known biochemical pathway diagrams and enzyme or
gene data.
It is estimated that only ¼ to ½ of endogenous
human metabolites in blood or urine have been
positively identified. Of those that have been
identified, very few have any information on
their normal concentration ranges. As part of
our newly funded Genome Canada
Fiona Bamforth Clin. Chemistry U of
Alberta Sample Acq.
Derrick Clive Chemistry U of Alberta Synthesis
Liang Li Chemistry. U of Alberta MS/Separation
Mike Ellison Biochemistry U of Alberta MS/Separati
on.