Bio-Rad GS-900™ Calibrated Densitometer - Manual (Page 66)

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2-D Electrophoresis Guide Appendices
Immunoblotting Blot detection by antibody binding
Immunodetection Detection of a molecule by its binding to an antibody
In-gel sample application Sample application to the IPG strip during IPG strip rehydration; may be passive
(In-gel rehydration)
or active (in the presence of a low applied voltage)
Ionic strength Measure of the ionic concentration of a solution that affects its resistance
Isoelectric Electrophoresis technique that separates proteins according to their
focusing (IEF) isoelectric point (pI)
Isoelectric point (pI) pH value at which a molecule carries no net electrical charge, or at which the
negative and positive charges are equal
Leading ion Ion in a discontinous buffer system with a greater mobility, typically Cl – (chloride ion)
MicroRotofor ™ cells Family of Bio-Rad sample preparation products, including the MicroRotofor
and kits liquid-phase IEF cell and MicroRotofor cell lysis kits
Monomer Unit that makes up a polymer (acrylamide is a monomer that is polymerized
into polyacrylamide)
Mini-PROTEAN ® cells Family of Bio-Rad products used for mini-format vertical electrophoresis;
and gels includes the Mini-PROTEAN Tetra and Mini-PROTEAN ® 3 Dodeca ™ cells
and Mini-PROTEAN precast gels
Molecular weight Mixtures of well-characterized or recombinant proteins used to help monitor
markers separation as well as estimate the size of the proteins separated in a gel
Ohm’s Law Describes the mutual dependence of three electrical parameters
(V, voltage; I, current; R, resistance): V = I × R
PAGE Polyacrylamide gel electrophoresis, a common method of separating proteins
based on molecular weight
PDQuest ™ software Bio-Rad’s 2-D gel analysis software
Polyacrylamide Anticonvective, sieving matrix used in gel electrophoresis. Polyacylamide gels
are cast using mixtures of acrylamide monomers with a cross-linking reagent,
usually N,N'-methylenebisacrylamide (bis), both dissolved in buffer
Polyacrylamide gel Electrophoresis technique that uses polyacrylamide as the separation medium
electrophoresis (PAGE)
PowerPac ™ Family of Bio-Rad power supplies
power supplies
Power supply Instrument that provides the electric power to drive electrophoresis
and electrophoretic blotting experiments
Precision Plus Protein ™ Bio-Rad’s family of recombinant molecular weight markers
standards
PROTEAN ® cells Family of Bio-Rad products used for large-format vertical electrophoresis
and isoelectric focusing; includes PROTEAN II xi, PROTEAN II XL,
PROTEAN
® Plus Dodeca ™ cells, and the PROTEAN ® i12 ™ IEF cell
ProteoMiner ™ beads, Protein enrichment technology that operates on the principle of dynamic range
reagents, and kits reduction; uses a bead-based library of combinatorial peptide ligands to enrich the
amounts of medium- and low-abundance proteins relative to high-abundance proteins
Prestained standards Mixture of molecular weight marker proteins that have covalently attached dye
molecules, which render the bands visible during electrophoresis and transfer
RC DC ™ assay kit Bio-Rad’s reductant- and detergent-compatible protein assay kit
ReadyStrip ™ IPG strips Bio-Rad’s brand of IPG strips
ReadyPrep ™ kits Bio-Rad’s brand of sample preparation and 2-D electrophoresis kits and reagents
R
f
value Relative distance a protein has traveled compared to the distance traveled by
the ion front. The R
f
value is used to compare proteins in different lanes and
even in different gels. It can be used with standards to generate standard curves,
from which the molecular weight or pI of an unknown may be estimated
Running buffer Buffer that provides the ions for the electrical current in an electrophoresis run.
It may also contain denaturing agents. The running buffer provides the trailing ions
in discontinuous electrophoresis
Sample solution Solution in which a sample is prepared or suspended prior to loading onto
an IPG strip
Sodium dodecyl sulfate Separation of molecules by molecular weight in a polyacrylamide gel matrix in
polyacrylamide gel
the presence of a denaturing detergent, such as sodium dodecyl sulfate (SDS).
electrophoresis SDS denatures polypeptides and binds to proteins at a constant charge-to-mass-ratio.
(SDS-PAGE) In a sieving polyacrylamide gel, the rate at which the resulting SDS-coated proteins
migrate in the gel is relative only to their size and not their charge or shape
Sodium dodecyl Anionic detergent that denatures proteins and binds to polypeptides in a constant
sulfate (SDS) weight ratio of 1.4 g/g of polypeptide (SDS:polypeptide)
Stain-free technology Protein detection technology involving UV-induced additive that modifies protein
tryptophan residues. Continued exposure to UV light causes fluorescence of the
modified proteins, which are then detected by a CCD imager. Sensitivity of this
technique is generally equal to or better than Coomassie staining
Stained standards Mixture of molecular weight marker proteins that have covalently attached dye
molecules; the bands are visible during electrophoresis and transfer
Standard Collection of molecules with known properties, such as molecular weight,
isoelectric point, or concentration. Often used to create standard curves,
from which the properties of an unknown may be determined
TGX ™ Bio-Rad’s Tris-glycine extended shelf life precast gels
Total protein stain Reagent that binds nonspecifically to proteins; used to detect the entire protein
pattern on a blot or gel
Trailing ion Ion in a discontinous buffer system with a lower mobility, typically glycinate
Tris Organic component of buffer solutions that has an effective buffering range of
pH 7.0–9.2; tris(hydroxymethyl)aminomethane
Triton X-100 Nonionic detergent widely used for protein solubilization
(for IEF and 2-D electrophoresis)
Tween 20 Nonionic detergent; used in blot detection procedures as a blocking reagent
or added to wash buffers to minimize nonspecific binding and background
Unstained standards Mixture of molecular weight marker proteins that do not have covalently attached
dye molecules; the bands are invisible during electrophoresis and transfer,
but are useful for molecular weight determination in stained gels
Urea Chaotrope usually included at rather high concentrations (9.5 M) in sample
solubilization buffers for denaturing IEF and 2-D PAGE
Volt-hour (Vh) Voltage multiplied by time is used as a unit for the duration of an IEF run
Western blotting Immobilization of proteins onto a membrane and subsequent detection by
protein-specific binding and detection reagents
Zwitterion Neutral molecule with positive and negative charges at different locations