Glossary

We have included a glossary to assist you during the course.

If you come across any other terms that you would like us to define, please add them to the comments.

Absolute quantification

The quantification of a metabolite through the use of internal standards and authentic chemical standards to accurately calculate a concentration for each metabolite.

Analyte

Is a chemical constituent of interest in an analytical procedure.

Anabolism

Utilises energy to synthesise molecules from smaller metabolic precursors, for example the synthesis of proteins from amino acids.

Anisotropic

A physical property that has a different value when measured in a different direction. For example, a peak in the chromatographic domain has a greater number of data points than measured in the mass domain.

Authentic chemical standard

An authentic chemical standard that is available to purchase or is synthesised and is applied in absolute quantification or to confirm the chemical identity of a metabolite.

Binning

To group or combine a number of values into a smaller number of bins, to reduce the number of data points.

Catabolism

The breakdown of organic substrates to provide energy in the form of adenosine triphosphate (ATP).

Chromatogram (mass)

The representation of mass spectrometry data on a chromatogram, where the x-axis represents the retention time and the y-axis represents the signal intensity.

Cofactor

A non-protein chemical compound that is required in addition to an enzyme for a metabolic reaction to be catalysed.

Database

A collection of data records that are organised in such a way that its contents can easily be managed, accessed, and updated.

Deconvolution

The construction of a data matrix from raw data files and defining each metabolite and peak area in each sample.

Direct infusion mass spectrometry (DIMS)

A method of sample introduction into a mass spectrometer – the liquid sample is continuously infused into the mass spectrometry.

Electrospray ionisation

A soft ionisation method applied to liquid samples that generates ions in the gas phase for mass analysis. The method imparts very small amounts of energy to the analytes and results in minimal source fragmentation.

Epigenetics

The study of the external modifications to DNA that turn genes on or off.

Feed-back loop

A control system in which the output of the system is routed back and acts as an input in to the circuit.

Feed-forward loop

A control system in which the output of an earlier step is fed into a step occurring further down the line.

Fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS)

A type of mass analyser for determining the mass-to-charge ratio of ions based on the cyclotron frequency of the ions in a fixed magnetic field.

Gas chromatography-mass spectrometry (GC-MS)

An analytical chemistry technique that combines gas chromatography and mass spectrometry to separate and analyse volatile and semi-volatile compounds.

Gene

A subunit of DNA that contains a set of instructions to encode a functional RNA or protein product.

Genome

The complement of genetic material of an organism.

Highly conserved

A highly conserved pathway is one that is present in a variety of species, for example glycolysis. The glycolysis pathway is common across may species and as one species gives rise to another the pathway is present and so is highly conserved.

Hydrophilic interaction liquid chromatography (HILIC)

A type of liquid chromatography that is commonly employed to separate water-soluble metabolites and is complementary to reversed-phase liquid chromatography. The stationary phase is water absorbed onto a hydrophobic silica-containing surface.

Hypothesis generating

The simultaneous analysis of a large number of biochemicals to gain new insights into how biochemicals interact at the global level.

Ionisation

The process by which an atom or molecule acquires a positive or negative charge by loosing or gaining electrons or gaining an ionic species to form ions.

Isomers

Two metabolites with the same molecular formulae and mass.

Liquid chromatography–mass spectrometry

An analytical technique that combines liquid chromatography and mass spectrometry to separates molecules according to hydrophobicity or hydrophilicity.

Mass accuracy

The degree to which a measured mass conforms to the theoretical mass.

Mass resolution

The ability to distinguish two peaks of slightly different mass-to-charge ratio (m/z) in a mass spectrum.

Mass Spectrometer

An analytical instrument applied to separate positively or negatively charged metabolites in time or space based on their mass to charge ratio (m/z).

Metabolically active sample

A sample that contains enzymes that catalyse the conversation of one metabolite to another.

Metabolic fingerprinting

The global, rapid and high-throughput analysis of crude (biological) samples or the metabolites extracted from biological samples for the high-throughput screening or classification of samples with minimal sample preparation.

Metabolic footprinting

Analysis of the extracellular metabolome (exometabolome) of an organism, for example, cell culture medium. The exometabolome will contain the metabolites the organism excretes or fails to take up from the environment.

Metabolic profiling

Analysis to identify and quantify metabolites related through similar chemistries or metabolic pathways. Normally employing chromatographic separation before detection with minimal sample preparation.

Metabolism

The term used to describe the collection of life-sustaining chemical reactions within the cells of living organisms.

Metabolite annotation

The data of a detected metabolite is matched to the theoretical properties of a metabolite.

Metabolite feature

A metabolite feature is a detected feature comprising of two or more reported parameters (mass, retention time, fragmentation spectrum). A single metabolite can be reported as multiple features, so the use of the term “feature” allows for the discrimination of a metabolite from the multiple products associated with the metabolite.

Metabolite identification

A detected metabolite is identified by comparing the parameters (mass-to-charge ratio, retention time, fragmentation spectra) to an authentic chemical standard.

Metabolites

The small molecular weight chemicals involved in metabolism such as glucose and ethanol.

Metabolome

The entire collection of low molecular weight compounds (metabolites) in a biological system.

Metabolomics

The unbiased identification and quantification of the entire collection of low molecular weight chemicals in a biological system.

Metabonomics

The quantitative measurement of the dynamic, multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification.

Metadata

A set of data that describes and provides information about the experimental samples and data.

Missing values

A value in which there is no data value present for the variable in the current observation.

Monoisotopic mass

The exact mass of the molecule calculated from the accurate mass of the most abundant isotope of each element.

Multivariate statistical analysis

A type of data analysis that takes into account more than one variable at the same time.

Nominal mass

The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer.

Nuclear magnetic resonance (NMR) spectroscopy

An analytical technique that exploits the magnetic properties of atomic nuclei to determine the physical and chemical properties of atoms or molecules.

Omics

A field of study within biology ending in –omics, including genomics, transcriptomics, proteomics and metabolomics.

Open access

Unrestricted access and reuse of research studies and data.

Orbital frequency

The number of times an ion moves in a circular motion (“orbits) every second.

Orbitrap

An mass analyser consisting of an outer-barrel-like electrode and an inner spindle-like electrode to trap ions in an orbital motion around the spindle.

Phenome

The complete set of phenotypes expressed by a cell, tissue, organ, organism or species.

Phenotype

The physical and biochemical characteristics of an organism as determined by the interaction of its genetic constituents and environment.

Protein

A large macromolecule that is composed of one or more chains of amino acids in the order specified by the base sequence of nucelotides in DNA.

Proteome

The entire collection of proteins in a biological system.

Quadrupole mass spectrometer

A type of mass spectrometer that consists of four parallel cylindrical rods, the sample ions are filtered based on their mass-to-charge ratio.

Quality control sample

A sample representing the quantitative and qualitative composition of the entire collection of samples.

Quenching

A procedure applied to stop metabolism.

Relative quantification

The comparison of the metabolite response (for example, chromatographic peak area) in one sample compared to that in another sample without defining the accurate concentration of the metabolite.

Repository

A central place that consists of a file system and one or multiple databases (i.e. meta data).

Retention time

The time taken for the metabolite to elute from the column after injection of the samples.

Reversed phase liquid chromatography

A type of liquid chromatography typically used to separate lipid metabolites. The stationary phase is hydrophobic and composed of long alkyl chains normally containing 8 or 18 carbons. This type of chromatography is complementary to hydrophilic interaction liquid chromatography.

Semi-targeted analytical approach

The identification and quantification of 100-200 metabolites, one calibration curve is used for a set of metabolites with the same chemical structure.

Spectral library

A curated and annotated collection of MS/MS spectra.

Stratified medicine

The separation of patients into group based on their risk of developing a disease or responding to a specific drug or treatment.

Substrate

Is the chemical that is being modified, so in metabolism where metabolite (1) is converted to metabolite (2) by an enzyme the substrate is metabolite 1.

Supervised data analysis

The assigning of data to a known biological class before computation.

Systems biology

A scientific strategy applied to study the complete system and how it relates to function or phenotype.

Targeted analysis

The absolute quantification and identification of one metabolite or a small number of metabolites. Significant sample preparation will be performed to separate the metabolites from the sample matrix.

Time-of-flight (ToF) mass spectrometer

A mass spectrometer that determines the mass-to-charge ratio via a time measurement.

Transcriptome

The entire collection of mRNA (transcripts) in a biological system.

Univariate data analysis

A method of data analysis that analyses one metabolite at a time.

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This article is from the free online course:

Metabolomics: Understanding Metabolism in the 21st Century

University of Birmingham