Detection proteins separated

A variety of methods are available to detect proteins separated by electrophoresis or to measure the concentration of total protein in a solution. These methods are normally based on the binding of a dye to one of the amino acids in protein, or a color reaction with an amino acid side chain. The most commonly used stains for protein detection on gels are Coomassie Brilliant Blue (98) and silver stain (99,100). These methods detect any protein residues, either in solution or on an electrophoresis gel. Their main requirement is sensitivity, not specificity. New, more sensitive dyes are being developed for the proteomic analysis of protein structure and sequence, for example Ruby Red (101). 

Some of the most sensitive procedures for detecting proteins separated by electrophoresis are based on immunological methods. After electrophoresis, proteins are transferred by blotting on to a membrane such as PVDF (Timmons and Dunbar 1990), and then detected by methods similar in principle to those described for the ELISA experiments. 

Sensitivity Silver stains currently offer the most sensitive non-radioactive method for detecting proteins separated by gel electrophoresis. They are 100-fold more sensitive than the Coomassie stains for most proteins (15-16). Chemical-development silver stains are in general, more sensitive than photo-development silver stains. This loss in senstivity may be compensated for by the ability of photo-development stain to produce an image within 10 to 15 minutes... 

Biochemical analyses of 6-OHDA-injected animals revealed a 93 percent depletion of dopamine. The tissue was assayed using electrochemical detection following separation by high-pressure liquid chromatography (Felice et al. 1978). recorded as ng/mg protein in the nucleus accumbens and compared to control rats with sham lesions (sham=65.5 4.4, lesion=4.9 1.5 t(39)=23.4). A lesion was defined as complete if 75 percent or more of the dopamine was determined to be depleted from the nucleus accumbens compared to mean sham group values. 

Western blot A method to detect protein in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate denatured proteins by mass. Some diagnostic applications for the Western blot include Lyme disease, bovine spongiform encephalopathy, and human immunodeficiency virus (HIV) (it is considered the gold standard for HIV diagnostic testing). 

For these reasons we have developed a different approach that measures differential expression of intact proteins.21 In this approach the proteins are extracted from the cell, separated on an HPLC column, ionized via electrospray, and automatically deconvoluted into their respective uncharged nominal masses. By this methodology it is then possible to obtain accurate, intact protein profiles of the individual strains of bacteria. Because the masses of the detected proteins are accurate to +2 Da from run to run, it is possible to subtract protein profiles from known strains to quickly identify differences in protein expression among newly mutated strains. 

Various methods have been used to examine the composition of proteins adsorbed to SAMs. Overall adsorption patterns can be examined with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) [50, 76, 77]. Absorbed proteins are eluted from the surface with surfactant (SDS), and then separated by electrophoresis. The proteins of interest are examined by western blotting [50, 76, 77]. Protein-specific antibodies can be used to detect proteins of... 

Figure 7.7. Results from model simulations showing the effect of protein separation and the effect of MS detection limit and MS dynamic range on the success rate and the relative dynamic range (RDR) for detection of proteins from H. sapiens tissue samples. (See page 219 for text discussion.)...

In the 1950s, new methods of protein separation were developed that enabled the systematic study of molecular variation in many more human proteins. Starch gel electrophoresis allowed the separation of closely related protein variants by differences in charge and molecular size. Smithies (1955) detected the amazing polymorphism of haptoglobin. In later years the method was extended to the study of allozymes (enzyme polymorphisms). 

Figure 3.23 Selectivity of phenyl and alkyl bonded stationary phase materials for protein separation. Column A, TSK gel phenyl-5PW RP, 75 mm x 4.6 mm i.d. B, TSK gel TMS 250, 75 mm x 4.6 mm i.d. eluent, 60 min linear gradient elution from 5% of 0.05% trifluoroacetic acid in 5%> aqueous acetonitrile to 80% of 0.05% trifluoroacetic acid in 80% aqueous acetonitrile flow rate, lml min-1 detection, UV 220 nm. Peaks 1, ribonuclease 2, insulin-, 3, cytochrome c 4, lysozyme-, 5, transferrin-, 6, bovine serum albumin-, 1, myoglobin-, and 8, ovalbumin.

In CZE, the capillary, inlet reservoir, and outlet reservoir are filled with the same electrolyte solution. This solution is variously termed background electrolyte, analysis buffer, or run buffer. In CZE, the sample is injected at the inlet end of the capillary, and components migrate toward the detection point according to their mass-to-charge ratio by the electrophoretic mobility and separations principles outlined in the preceding text. It is the simplest form of CE and the most widely used, particularly for protein separations. CZE is described in Capillary Zone Electrophoresis. ... 

The separation mechanism is quite different from other chromatographic techniques and a broader spectrum of possible impurities can be detected at the same system (e.g., inorganic small cations, anions by indirect detection, chiral separations by adding a chiral selector, proteins and peptides by adding a polymer to the separation buffer, etc.)... 

SDS-PAGE has traditionally been used as the primary method for size-based protein separations. SDS binds to polypeptide chains so that similar charge densities and constant mass-to-charge ratios of proteins are obtained. Then, electrophoretic separation of SDS-protein complexes based on size is achieved in a sieving medium. Detection of the separated... 

Most of the applications of HPLC for protein analysis deal with the storage proteins in cereals (wheat, corn, rice, oat, barley) and beans (pea, soybeans). HPLC has proved useful for cultivar identihcation, protein separation, and characterization to detect adulterations (illegal addition of common wheat flour to durum wheat flour) [107]. Recently Losso et al. [146] have reported a rapid method for rice prolamin separation by perfusion chromatography on a RP POROS RH/2 column (UV detection at 230nm), sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE), and molecular size determination by MALDl-MS. DuPont et al. [147] used a combination of RP-HPLC and SDS-PAGE to determine the composition of wheat flour proteins previously fractionated by sequential extraction. 

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