Last revised December 17, 2001
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Related glossaries include Mass Spectrometry, Proteins, Proteomics, Sequencing

2D gel electrophoresis:  Proteins are first separated across a gel according to their isoelectric point, then separated in a perpendicular direction on the basis of their molecular weight.  [CHI Proteomics]

Electrophoresis in which a second perpendicular electrophoretic transport is performed on the separate components resulting from the first electrophoresis.  Usually performed on polyacrylamide gels. [Metathesaurus] First introduced in 1975.  Most commonly used method for protein separation in proteomics.

2D gel databases See Databases & software directory.

affinity chromatography: A selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent. [IUPAC Biotech]

CE-MS (Capillary Electrophoresis- Mass Spectrometry):  Separation is achieved through channels etched on the surface of the capillary (connected to an external high- voltage power supply) which delivers sample to ESI- MS.  Automatable approach, with great sensitivity. [CHI Proteomics]

CIEF (Capillary electrophoresis IsoElectric Focusing):  Sample is “focused” in the capillary tube, both separating and concentrating the protein or peptide at its isoelectric point. Then the entire mixture is delivered to the mass spectrometer.  Using this technique the researchers have been able to record the molecular weight of all the proteins under study.  Can be used to separate proteins from microorganisms. [CHI Proteomics]

capillary array: A bundle of extremely narrow gel-filled tubes used to significantly speed the process of separating biological material. See capillary electrophoresis [ALSSA]

capillary electrochromatography: A rapidly evolving hybrid technique between HPLC and CE. In essence CE capillaries are packed with HPLC packing and a voltage is applied across the packed capillary which generates an electro-osmotic flow (EOF) [for example of EOF see the CE theory page of this website). The EOF transports solutes along the capillary towards the detector. Both differential partitioning and electrophoretic migration of the solutes occurs during their transportation towards the detector which leads to CEC separations. It is therefore possible to obtain unique separation selectivities using CEC compared to both HPLC and CE. ... The instrument used in CEC is identical to that used in CE - see below except that  a packed capillary is used. [Kevin D Altria, "CEC Theory"  www.ceandcec.com]  http://www.ceandcec.com/newpage5.htm

IUPAC has a Provisional recommendation on terminology. (July 2001)

capillary electromigration: IUPAC has a Provisional recommendation on terminology. (July 2001)

Capillary Electrophoresis (CE):  A separation technique in which a sample is introduced into a capillary tube and the compounds are separated by the first application of high voltage. [Metathesaurus]

capillary gel electrophoresis: Gel is in a capillary microchannel.  Improved quantification for highly complex samples.  Related term microcapillary electrophoresis. 

carrier ampholyte(s): Small soluble molecules that are capable of acting as an acid or a base. [CHI Proteomics] in standard ISO-DALT 2D gel electrophoresis.

chromatography: A physical method of separation in which the components to be separated are distributed between two phases, one of which is stationary (stationary phase) while the other (the mobile phase) moves in a definite direction. [IUPAC Compendium]

DGGE (Denaturing Gradient Gel Electrophoresis): A technique for screening for SNPs. [CHI SNP]

dHPLC denaturing high-performance liquid chromatography: Used in SNP- detection methods based on discrimination between perfect and mismatched hybridization, measures melting temperatures. (Mismatching results in lowered melting temperature.) This method involves passing the hybridization mixture through a chromatographic column several times at different temperatures and deriving the melting temperature from changes in the chromatogram. This method has the advantage of not needing labeled components; however, each assay requires at least 15 minutes to complete. [CHI SNP Update]

Edman degradation: A lab technique used to find out the order of amino acids in a polypeptide (chain of amino acids). It involves using the Edman reagent, phenyl isothiocyanate (PITC), to react one by one with each amino acid, in order. The technique is used in machines which automatically sequence (determine the order of subunits) polypeptides. [OMD]

electrophoresis:  The motion of colloidal particles in an electric field. [IUPAC Compendium]

Technique for separating and purifying molecules according to the relative distance they travel under the influence of an electric current. [NHLBI]

A method of separating large molecules (such as DNA fragments or proteins) from a mixture of similar molecules. An electric current is passed through a medium containing the mixture, and each kind of molecule travels through the medium at a different rate, depending on its electrical charge and size. Separation is based on these differences. Agarose and acrylamide gels are the media commonly used for electrophoresis of proteins and nucleic acids. [DOE]  

Related term gel electrophoresis.

Expanded Bed Adsorption EBA: What chromatographers need is a method that combines sample preparation with the first stage of chromatography. Welcome to expanded-bed adsorption (EBA) chromatography. EBA uses apparatus that is familiar to most users of standard liquid chromatography. The column has a flow adapter that is positioned to suit the specific step of resin preparation or protein purification. And a series of pumps and valves, connected through the adapter and bottom of the column, control the flow rate and direction of the buffer and sample loading (1, 2). Thus, it is feasible to perform preliminary EBA trials with a little ingenuity and standard chromatographic equipment. ...In the more traditional packed-bed methods, where the resin is confined between the bottom of the column and the flow adapter, clogging occurs when particulate matter and cell debris cannot flow around the closely packed resin beads. In contrast, EBA columns are fed from below, and the adapter is held away from the packed resin level, giving the resin room to expand and thus creating spaces between the beads. [Randall C. Willis "Expanded Bed Adsorption" Modern Drug Discovery 4 (12): 43-44 Dec. 2001]  http://pubs.acs.org/subscribe/journals/mdd/v04/i12/html/12toolbox.htm

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frontal affinity chromatography: Method for screening mixtures of compounds for affinity against an immobilised target. [IUPAC COMBINATORIAL CHEMISTRY]

gel electrophoresis: A DNA separation technique that is very important in DNA sequencing. Standard sequencing procedures involve cloning DNA fragments into special sequencing cloning vectors that carry tiny pieces of DNA. The next step is to determine the base sequence of the tiny fragments by a special procedure that generates a series of even tinier DNA fragments that differ in size by only one base. These nested fragments are separated by gel electrophoresis, in which the DNA pieces are added to a gelatinous solution, allowing the fragments to work their way down through the gel. Smaller pieces move faster and will reach the bottom first. Movement through the gel is hastened by applying an electrical field to the gel. [DOE]

Electrophoresis performed in a polymer matrix (gel) Broader term  electrophoresis, PAGE, SDS- PAGE.

gel shift: A method by which the interaction of a nucleic acid (DNA or RNA) with a protein is detected. The mobility of the nucleic acid is monitored in an agarose gel in the presence and absence of the protein: if the protein binds to the nucleic acid, the complex migrates more slowly in the gel (hence "gel shift"). A "supershift" allows determination of the specific protein, by virtue of a second shift in mobility that accompanies binding of a specific antibody to the nucleic acid-protein complex. [Lemon, Stanley M. and Alan Barbour "Glossary of terms commonly used in molecular biology" UNC- Chapel Hill and Univ. of Texas Health Science Center, US, 2000]  http://www.med.unc.edu/wrkunits/3ctrpgm/pmbb/mbt/GLOS.htm  

HPLC High Performance Liquid Chromatography: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed. [MeSH]

HPLC Glossary, Waters Corp. http://www.waters.com/menu.cfm?link=/Waters_Website/Corporate/glossary.htm

IEF (IsoElectric Focusing). Electrophoresis in which a pH gradient is established in a gel medium and integrated until they reach the site (or focus) at which the pH is equal to the isoelectric point. [Metathesaurus] First reported in 1961.  Earliest version used carrier ampholytes;  newer uses immobilized pH gradients. Compare with yeast two hybrid. Proteomics glossary

IPG (Immobilized pH Gradient). Now standard 2D gel electrophoresis method.  Amersham Pharmacia led commercialization effort. Can be used for pH range 3-12 and is method of choice for IsoElectric Focusing. [CHI Proteomics] Narrower term immobilized pH gradient shift.  

IPG-DALT: Immobilized pH Gradient with protein mass expressed in Daltons. [CHI Proteomics]

ISO-DALT: ISOelectric focusing electrophoresis, measured in Daltons.  Cannot resolve basic proteins with pI >7.0-7.5 pH. Use of isoelectric focusing greatly improves resolution. [CHI  Proteomics]

immobilized pH gradient shift: Introduction of gels with immobilized pH gradient (in 1982) improved the separability of 2D gel electrophoresis.  [CHI Proteomics] Narrower term IPG.

immobilized pH gradient strips, very narrow range: Also called “zoom gels” or proteomic contigs, used to improve sensitivity of 2D gel electrophoresis. [CHI Proteomics] Broader term IPG.

immunoprecipitation: Antibody based affinity purification. [CHI Proteomics]

in gel protein digestion: A method to cleave proteins into more easily identifiable peptide subunits directly in the gel immediately following separation of the proteins by gel electrophoresis. This method uses different enzymes, which specifically cleave between certain amino acid sequences. [ALSSA]

isoelectric point: The pH in solutions of proteins and related compounds at which the dipolar ions are at a maximum. [MeSH]

The pH value at which the net electric charge of an elementary entity is zero. pI is a commonly used symbol for this kind- of- quantity. It should be replaced by pH (I) because it is a pH determined under that particular condition. [IUPAC Compendium]

liquid chromatography LC: A separation technique in which the mobile phase is a liquid. Liquid chromatography can be carried out either in a column or on a plane. Present- day liquid chromatography generally utilizing very small particles and a relatively high inlet pressure is often characterized by the term high- performance (or high- pressure) liquid chromatography, and the acronym HPLC. [IUPAC Compendium]

microcapillary electrophoresis (micro-capillary electrophoresis): Is this different from microchip electrophoresis?

microchip electrophoresis: Microfabricated or chip (microchip electrophoresis) has achieved remarkably rapid development, and instrumentation continues to advance toward a fully automated tool. One of the applications in which microchip electrophoresis systems have had the biggest impact is in DNA separations, in large part because microchip electrophoresis offers some clear advantages over slab gel electrophoresis for automation, speed, and quantitative capability. [Steven M. Wishnies et. al. "Automated analysis of DNA fragments in Microchip Electrophoresis Systems" Pittcon Mar. 4-9, 2001 New Orleans LA, US]  http://pittcon.omnibooksonline.com/2001/papers/1722P.pdf

Microchip electrophoresis has revolutionized the field of capillary electrophoresis. We have demonstrated fundamental applications in DNA analysis on microchips as well as novel devices for high- throughput analysis. As one increases the feature density and separation performance of these devices it becomes necessary to fold the separation channel back on itself in a serpentine design. However, the turn portion of the channel has been shown to degrade separation performance, which has provided the impetus to investigate turn structures that allow channel- folding while maintaining the efficiency of the separation. [Brian Paegel's Research, Mathies Lab, Univ. of California- Berkeley US, 2000] http://www.cchem.berkeley.edu/~ramgrp/LabWebPage/Projects/Brian.html

non-denaturing gel electrophoresis: DNA fragments separate in a double stranded form.  Also known as “native gel” systems.  Related term IsoElectric Focusing.

pI:  See isoelectric point.

PAGE (PolyAcrylamide Gel Electrophoresis):  Electrophoresis in which a polyacrylamide gel is used as the diffusion medium. [Metathesaurus]  Narrower term SDS-PAGE.

protein affinity chromatography: As developed by Greenblatt, Alberts, and colleagues, has the disadvantage of requiring purified proteins as reagents, but it is superior to the two-hybrid approach because it generates fewer false positives and is more amenable to high-throughput screening. [Aled Edwards et al. “Proteomics: new tools for a new era” Modern Drug Discovery 3 (7): 35-44 Sept. 2000]

proteomic contigs: See immobilized pH gradient strip, very narrow range.

SDS-PAGE (Sodium Dodecyl Sulfate PolyAcrylamide Gel Electrophoresis):  May be helped by mass spectrometry, can be blotted or eluted for further chemical analysis i.e. Edman degradation, amino acid microsequencing or scanned MALDI-MS. Also known as denaturing gel electrophoresis or native gel electrophoresis. [Glick]  Broader term gel electrophoresis, PAGE.

Supercritical Fluid Chromatography SFC: SFC resembles HPLC, with most of the liquid mobile phase being replaced with dense carbon dioxide. SFC performs chromatographic separations by creating programmed composition gradients of methanol, or a less polar solvent, in carbon dioxide. For a comparable separation, these gradients make SFC three to five times faster than HPLC. In addition, the re-equilibration times are extremely fast, minimizing delay between runs. And speed benefits purity screening. [J. Smith & T. Berger "SFC A Better, Cheaper Purity Screener than HPLC" R&D Magazine, Sept. 2001] http://www.rdmag.com/features/0109hplc.asp

supershift: See under gel shift

tandem chromatography: [CHI Summit Proteomics]

two-D gel electrophoresis: See 2D gel electrophoresis

zoom gels: See immobilized pH gradient strips, very narrow range.

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.

Bibliography

Electrophoresis Society Glossary of  Terms (acronyms and abbreviations, to be expanded) 2000, 350+ terms http://www.aesociety.org/AESgloss.html

HPLC Glossary, Waters Corp. http://www.waters.com/menu.cfm?link=/Waters_Website/Corporate/glossary.htm

[IUPAC Chromatography] International Union of Pure and Applied Chemistry, Nomenclature for chromatography, L.S. Ettre, editor, Pure and Applied Chemistry 65: 819-872, 1993.  450+ definitions. http://www.merck.de/english/services/chromatographie/index.htm   Click on "IUPAC Nomenklatura"

Alpha glossary index