Bands containing proteins of interest can be excised from gels either by hand (for example, using a razor blade) or with the help of automated spot cutting systems, such as those commonly used in 2-D gel-based proteomics workflows. The proteins in the bands can then be either eluted from the gel piece (for example, by electroelution) or subjected to downstream processing (for example, tryptic digestion) while still in the gel.

Automated spot cutting instruments (spot cutters) are used to excise protein spots of interest from gels and to transfer them to microplates or other vessels for further analysis. Bio-Rad’s EXQuest™ spot cutter locates and excises protein bands or spots from 1-D and 2-D gels or blots and loads them into 96- and 384-well microplates or 96-tube racks for downstream processing and analysis.

The EXQuest spot cutter is designed to be both robust in construction and simple to operate, reducing manual labor and improving throughput of protein spots for analysis. It consists of an enclosure, an imaging system, a fluidics system, robotics, sensors, a cutting head, a gel tray, a microplate rack, and a wash station.

Versatile Excision Capability

The EXQuest spot cutter allows use of any common proteome separation and staining methods:

Freestanding 2-D and 1-D SDS-PAGE gels

Plastic- or glass-backed 2-D and 1-D gels

PVDF and nitrocellulose membrane blots

Gels or membranes stained for proteins with visible stains (such as silver and Coomassie blue stains) or fluorescent stains (such as Flamingo™ fluorescent gel stain and SYPRO Ruby protein stain)

Big Performance on the Bench

Accommodates any commercially available large or mini format gel or PVDF membrane blot in a small bench footprint

PDQuest software automatically selects spots in order from lowest to highest amount of protein, minimizing the chance of carryover contamination from spot to spot

Quantity One software provides convenient tools for 1–D gel cutting

Cutting tip produces precise cuts without damage or distortion on gels or PVDF membranes

Cuts up to 4 gels at a time at up to 600 spots per hour

System accuracy of ±0.1 mm ensures accurate excision of even small, closely grouped spots

Error-free data capture from image analysis to mass spectrometry

Built-in wash wells provide customized tip washing between cuts for extra contamination control

Quick-change settings to switch between UV and visible light modes

Compatible with ProteomeWorks™ and ProteomeWorks Plus spot cutters 

Fractionation by size (molecular weight) is an effective enrichment strategy for studies of protein families and posttranslational modifications, because the sizes of these proteins tend to be similar.

The Model 491 prep cell and the mini prep cell:

• Allow resolution of proteins differing in molecular weight by as little as 2%
• Separate up to 500 mg of total protein
• Can be used as a complementary separation strategy to 2-D gels as well as for downstream protein purification

The Model 491 prep cell has a sample capacity of 1–500 mg/0.5–15 ml, while the mini prep cell has a sample capacity of 0.5–1,000 µg/50–500 µl.

IEF works by applying an electric field to protein within a pH gradient. The proteins separate as they migrate through the pH gradient in response to the applied voltage. When a protein reaches a pH value that matches its pI, its net electrical charge becomes neutral, and stops migrating. In this way, each protein in a sample becomes "focused" according to its pI. IEF can be performed using two techniques: immobilized pH gradients (IPG) with ampholytes covalently bound to a gel, or carrier ampholytes that migrate through a gel to generate the pH gradient. This section provides technical details to perform successful IEF using IPG strips

When a protein is placed in a medium with a pH gradient and subjected to an electric field, it will initially move toward the electrode with the opposite charge. During migration through the pH gradient, the protein will either pick up or lose protons. As it migrates, its net charge and mobility will decrease and the protein will slow down. Eventually, the protein will arrive at the point where the pH gradient is equal to its pI. There, being uncharged, it will stop migrating (see figure below). If this protein should happen to diffuse to a region of lower pH, it will become protonated and be forced back toward the cathode by the electric field. If, on the other hand, it diffuses into a region of pH greater than its pI, the protein will become negatively charged and will be driven toward the anode. In this way, proteins condense, or are focused, into sharp bands in the pH gradient at their individual characteristic pI values.

This system designed to simultaneously run up to 12 immobilized pH gradient (IPG) strips in 12 independently programmed lanes, which allows users to confidently run 12 different conditions at one time. Although many available IEF systems have multiple lanes, all but the PROTEAN i12 system depend on a single power supply, allowing only one set of conditions to be run at a time.

IEF can be run under either native or denaturing conditions. Native IEF retains protein structure and enzymatic activity. However, denaturing IEF is performed in the presence of high concentrations of urea, which dissociates proteins into individual subunits and abolishes secondary and tertiary structures. Whereas native IEF may be a more convenient option because it can be performed with a variety of precast gels, denaturing IEF often offers higher resolution and is more suitable for the analysis of complex protein mixtures.

   Focusing is a steady-state mechanism with regard to pH. Proteins approach their respective pI values at differing rates, but remain relatively fixed at those pH values for extended periods. By contrast, proteins in conventional electrophoresis continue to move through the medium until the electric field is removed. Moreover, in IEF, proteins migrate to their steady-state positions from anywhere in the system.

Reference:

1. Westermeier R (2004). Isoelectric focusing. Methods Mol Biol 244, 225–232.

Features include:

• Transmissive and reflective imaging using red, green, and blue CCD technology to scan chromogenic samples at the optimal detection wavelength
• Imaging of a wide variety of samples such as 1-D and 2-D gels, colorimetric dot and slot blots, film-based chemiluminescent blots, autoradiograms, slides, and photographs
• IQ/OQ for verification of the reflectance and transmittance calibration functions
• High resolution and analysis of closest bands on a gel due to 12-bit precision and 36.3 μm resolution
• Scanning of larger gels for enhanced separation of proteins on oversized 29 x 40 cm sample platen
• Accurate quantitation of samples, such as Coomassie Blue– and silver-stained gels, over a large dynamic range (0–3.0 OD)
• Sealed imaging platen to accommodate wet samples of variable thickness
• Purity analysis and lane background tools for manufacturing QC

Transmittance and Reflectance

Unlike laser densitometer systems, the GS-800 calibrated densitometer has both transmittance and true reflectance capabilities that allow accurate scans of both transparent and opaque samples. The advantage of true reflectance scanning is accurate detection and analysis of molecules on the surface of membranes, rather than molecules distributed throughout the membrane matrix. True reflectance provides the most accurate detection and analysis of dot blots, slot blots, and other electrophoretic blots without quantitation error.