The<unk>  method is composed of a gel electrophoresis to separate native proteins by 3-D structure or denatured proteins by the length of the polypeptide, followed by an electrophoretic transfer onto a membrane (mostly PVDF or nitrocellulose) and an immunostaining procedure to visualize a certain protein on the<unk>  membrane. SDS-PAGE is generally used for the denaturing electrophoretic separation of proteins. SDS is generally used as a buffer (as well as in the gel) in order to give all proteins present a uniform negative charge, since proteins can be positively, negatively, or neutrally charged. This type of electrophoresis is known as SDS-PAGE (SDS-polyacrylamide gel electrophoresis). Prior to electrophoresis, protein samples are often boiled to denature the proteins present. This ensures that proteins are separated based on size and prevents proteases (enzymes that break down proteins) from degrading samples. Following electrophoretic separation, the proteins are transferred to a membrane (typically nitrocellulose or PVDF). The membrane is often then stained with Ponceau S in order to visualize the proteins on the<unk>  and ensure a proper transfer occurred. Next the proteins are blocked with milk (or other blocking agents) to prevent non-specific antibody binding, and then stained with antibodies specific to the target protein. Lastly, the membrane will be stained with a secondary antibody that recognizes the first antibody staining, which can then be used for detection by a variety of methods. The gel electrophoresis step is included in<unk>  analysis to resolve the issue of the cross-reactivity of antibodies. Gel electrophoresis The proteins of the sample are separated using gel electrophoresis. Separation of proteins may be by isoelectric point (pI), molecular weight, electric charge, or a combination of these factors. The nature of the separation depends on the treatment of the sample and the nature of the gel. By far the most common type of gel electrophoresis employs polyacrylamide gels and buffers loaded with sodium dodecyl sulfate (SDS). SDS-PAGE (SDS polyacrylamide gel electrophoresis) maintains polypeptides in a denatured state once they have been treated with strong reducing agents to remove secondary and tertiary structure (e.g. disulfide bonds S-S to sulfhydryl groups SH and SH) and thus allows separation of proteins by their molecular mass. Sampled proteins become covered in the negatively charged SDS, effectively becoming anionic, and migrate towards the positively charged (higher voltage) anode (usually having a red wire) through the acrylamide mesh of the gel. Smaller proteins migrate faster through this mesh, and the proteins are thus separated according to size (usually measured in kilodaltons, kDa). The concentration of acrylamide determines the resolution of the gel – the greater the acrylamide concentration, the better the resolution of lower molecular weight proteins. The lower the acrylamide concentration, the better the resolution of higher molecular weight proteins. Proteins travel only in one dimension along the gel for most<unk> s. Samples are loaded into wells in the gel. One lane is usually reserved for a marker or ladder, which is a commercially available mixture of proteins of known molecular weights, typically stained so as to form visible, coloured bands. When voltage is applied along the gel, proteins migrate through it at different speeds dependent on their size. These different rates of advancement (different electrophoretic mobilities) separate into bands within each lane. Protein bands can then be compared to the ladder bands, allowing estimation of the protein's molecular weight. SDS-PAGE electrophoresis It is also possible to use a two-dimensional gel which spreads the proteins from a single sample out in two dimensions. Proteins are separated according to isoelectric point (pH at which they have a neutral net charge) in the first dimension, and according to their molecular weight in the second dimension. Transfer To make the proteins accessible to antibody detection, they are moved from within the gel onto a membrane, a solid support, it’s an essential part of the process. There are two types of membrane: nitrocellulose (NC) or polyvinylidene difluoride (PVDF). NC membrane has high affinity for protein and its retention abilities. However, NC is brittle, and does not allow the<unk>  to be used for re-probing, whereas PVDF membrane allows the<unk>  to be re-probed. The most commonly used method for transferring the proteins is called electroblotting. Electroblotting uses an electric current to pull the negatively charged proteins from the gel towards the positively charged anode, and into the PVDF or NC membrane. The proteins move from within the gel onto the membrane while maintaining the organization they had within the gel. An older method of transfer involves placing a membrane on top of the gel, and a stack of filter papers on top of that. The entire stack is placed in a buffer solution which moves up the paper by capillary action, bringing the proteins with it. In practice this method is not commonly used due to the lengthy procedure time. As a result of either transfer process, the proteins are exposed on a thin membrane layer for detection. Both varieties of membrane are chosen for their non-specific protein binding properties (i.e. binds all proteins equally well). Protein binding is based upon hydrophobic interactions, as well as charged interactions between the membrane and protein. Nitrocellulose membranes are cheaper than PVDF, but are far more fragile and cannot withstand repeated probings.<unk>  transfer Total protein staining Total protein staining allows the total protein that has been successfully transferred to the membrane to be visualised, allowing the user to check the uniformity of protein transfer and to perform subsequent normalization of the target protein with the actual protein amount per lane. Normalization with the so-called "loading control" was based on immunostaining of housekeeping proteins in the classical procedure, but is heading toward total protein staining recently, due to multiple benefits. At least seven different approaches for total protein staining have been described for<unk>  normalization: Ponceau S, stain-free techniques, Sypro Ruby, Epicocconone, Coomassie R-350, Amido Black, and Cy5. In order to avoid noise of signal, total protein staining should be performed before blocking of the membrane. Nevertheless, post-antibody stainings have been described as well. Blocking Since the membrane has been chosen for its ability to bind protein and as both antibodies and the target are proteins, steps must be taken to prevent the interactions between the membrane and the antibody used for detection of the target protein. Blocking of non-specific binding is achieved by placing the membrane in a dilute solution of protein – typically 3–5% bovine serum albumin (BSA) or non-fat dry milk (both are inexpensive) in tris-buffered saline (TBS) or I-Block, with a minute percentage (0.1%) of detergent such as Tween 20 or Triton X-100. Although non-fat dry milk is preferred due to its availability, an appropriate blocking solution is needed as not all proteins in milk are compatible with all the detection bands. The protein in the dilute solution attaches to the membrane in all places where the target proteins have not attached. Thus, when the antibody is added, it cannot bind to the membrane, and therefore the only available binding site is the specific target protein. This reduces background in the final product of the<unk> , leading to clearer results, and eliminates false positives. Incubation During the detection process the membrane is "probed" for the protein of interest with a modified antibody which is linked to a reporter enzyme; when exposed to an appropriate substrate, this enzyme drives a colorimetric reaction and produces a color. For a variety of reasons, this traditionally takes place in a two-step process, although there are now one-step detection methods available for certain applications. Primary antibody The primary antibodies are generated when a host species or immune cell culture is exposed to the protein of interest (or a part thereof). Normally, this is part of the immune response, whereas here they are harvested and used as sensitive and specific detection tools that bind the protein directly. After blocking, a solution of primary antibody (generally between 0.5 and 5 micrograms/mL) diluted in either PBS or TBST wash buffer is incubated with the membrane under gentle agitation for typically an hour at room temperature, or overnight at 4°C. It can also be incubated at different temperatures, with lesser temperatures being associated with more binding, both specific (to the target protein, the "signal") and non-specific ("noise"). Following incubation, the membrane is washed several times in wash buffer to remove unbound primary antibody, and thereby minimize background. Typically, the wash buffer solution is composed of buffered saline solution with a small percentage of detergent, and sometimes with powdered milk or BSA. Secondary antibody After rinsing the membrane to remove unbound primary antibody, the membrane is exposed to another antibody known as the secondary antibody. Antibodies come from animal sources (or animal sourced hybridoma cultures). The secondary antibody recognises and binds to the species-specific portion of the primary antibody. Therefore, an anti-mouse secondary antibody will bind to almost any mouse-sourced primary antibody, and can be referred to as an 'anti-species' antibody (e.g. anti-mouse, anti-goat etc.). To allow detection of the target protein,
Western blot
Immunolabeling
Immunoassay
MALDI imaging
Ink blot test
Magnetic immunoassay
Radioimmunoassay
Immunostaining