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The metabolome refers to the complete set of
small-molecule Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs ar ...
chemicals found within a biological sample. The biological sample can be a
cell Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Locations * Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery ...
, a cellular organelle, an organ, a tissue, a tissue extract, a
biofluid Body fluids, bodily fluids, or biofluids, sometimes body liquids, are liquids within the human body. In lean healthy adult men, the total body water is about 60% (60–67%) of the total Human body weight, body weight; it is usually slightly lower ...
or an entire
organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...
. The
small molecule Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs ar ...
chemicals found in a given metabolome may include both endogenous
metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, ...
that are naturally produced by an
organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...
(such as amino acids,
organic acids An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH. Sulfonic acids, containing the group –SO2OH, are r ...
,
nucleic acids Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...
,
fatty acids In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with an aliphatic chain, which is either saturated and unsaturated compounds#Organic chemistry, saturated or unsaturated. Most naturally occurring fatty acids have an B ...
,
amines In chemistry, amines (, ) are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia (), wherein one or more hydrogen atoms have been replaced by a substituent such ...
,
sugars Sugar is the generic name for sweet-tasting, soluble carbohydrates, many of which are used in food. Simple sugars, also called monosaccharides, include glucose, fructose, and galactose. Compound sugars, also called disaccharides or double ...
,
vitamins A vitamin is an organic molecule (or a set of molecules closely related chemically, i.e. vitamers) that is an essential micronutrient that an organism needs in small quantities for the proper functioning of its metabolism. Essential nutrien ...
, co-factors,
pigments A pigment is a colored material that is completely or nearly insoluble in water. In contrast, dyes are typically soluble, at least at some stage in their use. Generally dyes are often organic compounds whereas pigments are often inorganic compoun ...
,
antibiotics An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting bacterial infections, and antibiotic medications are widely used in the treatment and prevention o ...
, etc.) as well as exogenous chemicals (such as drugs, environmental contaminants,
food additives Food additives are substances added to food to preserve flavor or enhance taste, appearance, or other sensory qualities. Some additives have been used for centuries as part of an effort to preserve food, for example vinegar (pickling), salt (sal ...
, toxins and other
xenobiotics A xenobiotic is a chemical substance found within an organism that is not naturally produced or expected to be present within the organism. It can also cover substances that are present in much higher concentrations than are usual. Natural compo ...
) that are not naturally produced by an organism. In other words, there is both an endogenous metabolome and an exogenous metabolome. The endogenous metabolome can be further subdivided to include a "primary" and a "secondary" metabolome (particularly when referring to plant or microbial metabolomes). A
primary metabolite A primary metabolite is a kind of metabolite that is directly involved in normal growth, development, and reproduction. It usually performs a physiological function in the organism (i.e. an intrinsic function). A primary metabolite is typically pr ...
is directly involved in the normal growth, development, and reproduction. A
secondary metabolite Secondary metabolites, also called specialised metabolites, toxins, secondary products, or natural products, are organic compounds produced by any lifeform, e.g. bacteria, fungi, animals, or plants, which are not directly involved in the norma ...
is not directly involved in those processes, but usually has important ecological function.
Secondary metabolites Secondary metabolites, also called specialised metabolites, toxins, secondary products, or natural products, are organic compounds produced by any lifeform, e.g. bacteria, fungi, animals, or plants, which are not directly involved in the nor ...
may include
pigments A pigment is a colored material that is completely or nearly insoluble in water. In contrast, dyes are typically soluble, at least at some stage in their use. Generally dyes are often organic compounds whereas pigments are often inorganic compoun ...
,
antibiotics An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting bacterial infections, and antibiotic medications are widely used in the treatment and prevention o ...
or waste products derived from partially metabolized
xenobiotics A xenobiotic is a chemical substance found within an organism that is not naturally produced or expected to be present within the organism. It can also cover substances that are present in much higher concentrations than are usual. Natural compo ...
. The study of the metabolome is called
metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...
.


Origins

The word metabolome appears to be a blending of the words "
metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...
" and "
chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
". It was constructed to imply that
metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, ...
are indirectly encoded by genes or act on genes and gene products. The term "metabolome" was first used in 1998 and was likely coined to match with existing biological terms referring to the complete set of genes (the
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
), the complete set of proteins (the
proteome The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. ...
) and the complete set of transcripts (the
transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The t ...
). The first book on
metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...
was published in 2003. The first journal dedicated to metabolomics (titled simply "Metabolomics") was launched in 2005 and is currently edited by Prof.
Roy Goodacre Royston "Roy" Goodacre is Chair in Biological Chemistry at the University of Liverpool. With training in both Microbiology and Pyrolysis- Mass Spectrometry, Goodacre runs a multidisciplinary Metabolomics and Raman spectroscopy research gro ...
. Some of the more significant early papers on metabolome analysis are listed in the references below.


Measuring the metabolome

The metabolome reflects the interaction between an organism's genome and its environment. As a result, an organism's metabolome can serve as an excellent probe of its
phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...
(i.e. the product of its
genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...
and its environment).
Metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, ...
can be measured (identified, quantified or classified) using a number of different technologies including
NMR spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fie ...
and mass spectrometry. Most mass spectrometry (MS) methods must be coupled to various forms of
liquid chromatography In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system (a ...
(LC), gas chromatography (GC) or
capillary electrophoresis Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other elect ...
(CE) to facilitate compound separation. Each method is typically able to identify or characterize 50-5000 different metabolites or metabolite "features" at a time, depending on the instrument or protocol being used. Currently it is not possible to analyze the entire range of metabolites by a single analytical method.
Nuclear magnetic resonance (NMR) spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fie ...
is an analytical chemistry technique that measures the absorption of
radiofrequency Radio frequency (RF) is the oscillation rate of an alternating electric current or voltage or of a magnetic, electric or electromagnetic field or mechanical system in the frequency range from around to around . This is roughly between the upper ...
radiation of specific nuclei when molecules containing those nuclei are placed in strong
magnetic fields A magnetic field is a vector field that describes the magnetic influence on moving electric charges, electric currents, and magnetic materials. A moving charge in a magnetic field experiences a force perpendicular to its own velocity and to ...
. The frequency (i.e. the
chemical shift In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of an atomic nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure o ...
) at which a given atom or nucleus absorbs is highly dependent on the chemical environment (bonding, chemical structure nearest neighbours, solvent) of that atom in a given molecule. The NMR absorption patterns produce "resonance" peaks at different frequencies or different chemical shifts – this collection of peaks is called an
NMR spectrum Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fie ...
. Because each chemical compound has a different chemical structure, each compound will have a unique (or almost unique)
NMR spectrum Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fie ...
. As a result, NMR is particularly useful for the characterization, identification and quantification of small molecules, such as metabolites. The widespread use of NMR for "classical" metabolic studies, along with its exceptional capacity to handle complex metabolite mixtures is likely the reason why NMR was one of the first technologies to be widely adopted for routine metabolome measurements. As an analytical technique, NMR is non-destructive, non-biased, easily quantifiable, requires little or no separation, permits the identification of novel compounds and it needs no chemical derivatization. NMR is particularly amenable to detecting compounds that are less tractable to LC-MS analysis, such as sugars, amines or volatile liquids or GC-MS analysis, such as large molecules (>500 Da) or relatively non-reactive compounds. NMR is not a very sensitive technique with a lower limit of detection of about 5 μM. Typically 50-150 compounds can be identified by NMR-based metabolomic studies. Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of molecules. Molecules or molecular fragments are typically charged or ionized by spraying them through a charged field (
electrospray ionization Electrospray ionization (ESI) is a technique used in mass spectrometry to produce ions using an electrospray in which a high voltage is applied to a liquid to create an aerosol. It is especially useful in producing ions from macromolecules becaus ...
), bombarding them with electrons from a hot filament ( electron ionization) or blasting them with a laser when they are placed on specially coated plates (matrix assisted laser desorption ionization). The charged molecules are then propelled through space using electrodes or magnets and their speed, rate of curvature, or other physical characteristics are measured to determine their mass-to-charge ratio. From these data the mass of the parent molecule can be determined. Further fragmentation of the molecule through controlled collisions with gas molecules or with electrons can help determine the structure of molecules. Very accurate mass measurements can also be used to determine the elemental formulas or elemental composition of compounds. Most forms of mass spectrometry require some form of separation using
liquid chromatography In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system (a ...
or gas chromatography. This separation step is required to simplify the resulting mass spectra and to permit more accurate compound identification. Some mass spectrometry methods also require that the molecules be derivatized or chemically modified so that they are more amenable for
chromatographic In chemical analysis, chromatography is a laboratory technique for the separation of a mixture into its components. The mixture is dissolved in a fluid solvent (gas or liquid) called the ''mobile phase'', which carries it through a system (a ...
separation (this is particularly true for GC-MS). As an analytical technique, MS is a very sensitive method that requires very little sample (<1 ng of material or <10 μL of a biofluid) and can generate signals for thousands of metabolites from a single sample. MS instruments can also be configured for very high throughput metabolome analyses (hundreds to thousands of samples a day). Quantification of metabolites and the characterization of novel compound structures is more difficult by MS than by NMR. LC-MS is particularly amenable to detecting hydrophobic molecules (
lipids Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include ...
,
fatty acids In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with an aliphatic chain, which is either saturated and unsaturated compounds#Organic chemistry, saturated or unsaturated. Most naturally occurring fatty acids have an B ...
) and peptides while GC-MS is best for detecting
small molecules Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs ...
(<500 Da) and highly volatile compounds (
esters In chemistry, an ester is a compound derived from an oxoacid (organic or inorganic) in which at least one hydroxyl group () is replaced by an alkoxy group (), as in the substitution reaction of a carboxylic acid and an alcohol. Glycerides are ...
,
amines In chemistry, amines (, ) are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia (), wherein one or more hydrogen atoms have been replaced by a substituent such ...
, ketones,
alkanes In organic chemistry, an alkane, or paraffin (a historical trivial name that also has other meanings), is an acyclic saturated hydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in whi ...
,
thiols In organic chemistry, a thiol (; ), or thiol derivative, is any organosulfur compound of the form , where R represents an alkyl or other organic substituent. The functional group itself is referred to as either a thiol group or a sulfhydryl grou ...
). Unlike the
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
or even the
proteome The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. ...
, the metabolome is a highly dynamic entity that can change dramatically, over a period of just seconds or minutes. As a result, there is growing interest in measuring metabolites over multiple time periods or over short time intervals using modified versions of NMR or MS-based metabolomics.


Metabolome databases

Because an organism's metabolome is largely defined by its
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
, different species will have different metabolomes. Indeed, the fact that the metabolome of a tomato is different than the metabolome of an apple is the reason why these two fruits taste so different. Furthermore, different tissues, different
organs In biology, an organ is a collection of tissues joined in a structural unit to serve a common function. In the hierarchy of life, an organ lies between tissue and an organ system. Tissues are formed from same type cells to act together in a f ...
and biofluids associated with those organs and tissues can also have distinctly different metabolomes. The fact that different organisms and different tissues/ biofluids have such different metabolomes has led to the development of a number of organism-specific and biofluid-specific metabolome databases. Some of the better known metabolome databases include the
Human Metabolome Database The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. Created by the Human Metabolome Project funded by Genome Canada. One of the first d ...
or HMDB, the Yeast Metabolome Database or
YMDB The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB was designed to facilitate yeast me ...
, the E. coli Metabolome Database or ECMDB, the Arabidopsis metabolome database or AraCyc as well as the Urine Metabolome Database, the
Cerebrospinal Fluid Cerebrospinal fluid (CSF) is a clear, colorless body fluid found within the tissue that surrounds the brain and spinal cord of all vertebrates. CSF is produced by specialised ependymal cells in the choroid plexus of the ventricles of the ...
(CSF) Metabolome Database and the Serum Metabolome Database. The latter three databases are specific to human biofluids. A number of very popular general metabolite databases also exist including
KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...
, MetaboLights, the
Golm Metabolome Database The Golm Metabolome Database (GMD) is a gas chromatography–mass spectrometry, gas chromatography (GC) – mass spectrometry (MS) reference library dedicated to metabolite profiling experiments and comprises mass spectral and retention index (R ...
,
MetaCyc The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information ...
, LipidMaps and Metlin. Metabolome databases can be distinguished from metabolite databases in that metabolite databases contain lightly annotated or synoptic metabolite data from multiple organisms while metabolome databases contain richly detailed and heavily referenced chemical, pathway, spectral and metabolite concentration data for specific organisms.


The Human Metabolome Database

The
Human Metabolome Database The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. Created by the Human Metabolome Project funded by Genome Canada. One of the first d ...
is a freely available, open-access database containing detailed data on more than 40,000 metabolites that have already been identified or are likely to be found in the human body. The HMDB contains three kinds of information: 1) chemical information, 2) clinical information, and 3) biochemical information. The chemical data includes >40,000 metabolite structures with detailed descriptions, extensive chemical classifications, synthesis information and observed/calculated chemical properties. It also contains nearly 10,000 experimentally measured
NMR Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with ...
, GC-MS and LC/MS spectra from more than 1100 different metabolites. The clinical information includes data on >10,000
metabolite In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...
-
biofluid Body fluids, bodily fluids, or biofluids, sometimes body liquids, are liquids within the human body. In lean healthy adult men, the total body water is about 60% (60–67%) of the total Human body weight, body weight; it is usually slightly lower ...
concentrations, metabolite concentration information on more than 600 different human diseases and pathway data for more than 200 different inborn errors of metabolism. The biochemical information includes nearly 6000 protein (and DNA) sequences and more than 5000 biochemical reactions that are linked to these metabolite entries. The HMDB supports a wide variety of online queries including text searches, chemical structure searches, sequence similarity searches and spectral similarity searches. This makes it particularly useful for metabolomic researchers who are attempting to identify or understand metabolites in clinical metabolomic studies. The first version of the HMDB was released in Jan. 1 2007 and was compiled by scientists at the
University of Alberta The University of Alberta, also known as U of A or UAlberta, is a Public university, public research university located in Edmonton, Alberta, Canada. It was founded in 1908 by Alexander Cameron Rutherford,"A Gentleman of Strathcona – Alexande ...
and the
University of Calgary The University of Calgary (U of C or UCalgary) is a public research university located in Calgary, Alberta, Canada. The University of Calgary started in 1944 as the Calgary branch of the University of Alberta, founded in 1908, prior to being ins ...
. At that time they reported data on 2,500
metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, ...
, 1,200 drugs and 3,500 food components. Since then these scientists have greatly expanded the collection. The latest version of the HMDB (version 3.5) contains >16,000 endogenous metabolites, >1500 drugs and >22,000 food constituents or food metabolites.


Human biofluid metabolomes

Scientists at the
University of Alberta The University of Alberta, also known as U of A or UAlberta, is a Public university, public research university located in Edmonton, Alberta, Canada. It was founded in 1908 by Alexander Cameron Rutherford,"A Gentleman of Strathcona – Alexande ...
have been systematically characterizing specific biofluid metabolomes including the serum metabolome, the urine metabolome, the
cerebrospinal fluid Cerebrospinal fluid (CSF) is a clear, colorless body fluid found within the tissue that surrounds the brain and spinal cord of all vertebrates. CSF is produced by specialised ependymal cells in the choroid plexus of the ventricles of the ...
(CSF) metabolome and the saliva metabolome. These efforts have involved both experimental metabolomic analysis (involving
NMR Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with ...
, GC-MS,
ICP-MS Inductively coupled plasma mass spectrometry (ICP-MS) is a type of mass spectrometry that uses an inductively coupled plasma to ionize the sample. It atomizes the sample and creates atomic and small polyatomic ions, which are then detected. It is ...
, LC-MS and HPLC assays) as well as extensive literature mining. According to their data, the human serum metabolome contains at least 4200 different compounds (including many lipids), the human urine metabolome contains at least 3000 different compounds (including hundreds of volatiles and gut microbial metabolites), the human CSF metabolome contains nearly 500 different compounds while the human saliva metabolome contains approximately 400 different metabolites, including many bacterial products.


Yeast Metabolome Database

The Yeast Metabolome Database is a freely accessible, online database of >2000 small molecule metabolites found in or produced by
Saccharomyces cerevisiae ''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungus microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...
(
Baker's yeast Baker's yeast is the common name for the strains of yeast commonly used in baking bread and other bakery products, serving as a leavening agent which causes the bread to rise (expand and become lighter and softer) by converting the fermentabl ...
). The
YMDB The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB was designed to facilitate yeast me ...
contains two kinds of information: 1) chemical information and 2) biochemical information. The chemical information in YMDB includes 2027 metabolite structures with detailed metabolite descriptions, extensive chemical classifications, synthesis information and observed/calculated chemical properties. It also contains nearly 4000
NMR Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with ...
, GC-MS and LC/MS spectra obtained from more than 500 different metabolites. The biochemical information in
YMDB The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB was designed to facilitate yeast me ...
includes >1100 protein (and DNA) sequences and >900 biochemical reactions. The
YMDB The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (Baker’s yeast). The YMDB was designed to facilitate yeast me ...
supports a wide variety of queries including text searches, chemical structure searches, sequence similarity searches and spectral similarity searches. This makes it particularly useful for metabolomic researchers who are studying yeast as a model organism or who are looking into optimizing the production of fermented beverages (wine, beer).
Secondary electrospray ionization Secondary electro-spray ionization (SESI) is an ambient ionization technique for the analysis of trace concentrations of vapors, where a nano-electrospray produces charging agents that collide with the analyte molecules directly in gas-phase. In t ...
- high resolution mass spectrometry SESI-HRMS is a non-invasive analytical technique that allows us to monitor the yeast metabolic activities. SESI-HRMS has found around 300 metabolites in the yeast fermentation process, this suggests that a large number of glucose metabolites are not reported in the literature.


The Escherichia coli Metabolome Database

The E. Coli Metabolome Database is a freely accessible, online database of >2700 small molecule metabolites found in or produced by
Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...
(E. coli strain K12, MG1655). The ECMDB contains two kinds of information: 1) chemical information and 2) biochemical information. The chemical information includes more than 2700 metabolite structures with detailed metabolite descriptions, extensive chemical classifications, synthesis information and observed/calculated chemical properties. It also contains nearly 5000
NMR Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with ...
, GC-MS and LC-MS spectra from more than 600 different metabolites. The biochemical information includes >1600 protein (and DNA) sequences and >3100 biochemical reactions that are linked to these metabolite entries. The ECMDB supports many different types of online queries including text searches, chemical structure searches, sequence similarity searches and spectral similarity searches. This makes it particularly useful for metabolomic researchers who are studying E. coli as a model organism.
Secondary electrospray ionization Secondary electro-spray ionization (SESI) is an ambient ionization technique for the analysis of trace concentrations of vapors, where a nano-electrospray produces charging agents that collide with the analyte molecules directly in gas-phase. In t ...
(SESI-MS) can discriminate between eleven E. Coli strains thanks to the volatile organic compound profiling.


Metabolome atlas of the aging mouse brain

In 2021, the first brain metabolome atlas of the mouse brain – and of an animal (a mammal) across different life stages – was released online. The data differentiates by brain regions and the metabolic changes could be "mapped to existing gene and protein brain atlases".


See also

* Tumor metabolome *
Protein electrophoresis Protein electrophoresis is a method for analysing the proteins in a fluid or an extract. The electrophoresis may be performed with a small volume of sample in a number of alternative ways with or without a supporting medium: SDS polyacrylamide gel ...
*
Protein sequencing Protein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing o ...


References


External links

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