In-gel digestion

The in-gel digestion step is a part of the sample preparation for the mass spectrometric identification of proteins in course of proteomic analysis. The method was introduced in 1992 by Rosenfeld. Innumerable modifications and improvements in the basic elements of the procedure remain. The in-gel digestion step is a part of the sample preparation for the mass spectrometric identification of proteins in course of proteomic analysis. The method was introduced in 1992 by Rosenfeld. Innumerable modifications and improvements in the basic elements of the procedure remain. The in-gel digestion step primarily comprises the four steps; destaining, reduction and alkylation (R&A) of the cysteines in the protein, proteolytic cleavage of the protein and extraction of the generated peptides. Proteins which were separated by 1D or 2D PAGE are usually visualised by staining with dyes like Coomassie Brilliant Blue (CBB) or silver. Although the sensitivity of the method is significantly lower, the use of Coomassie is more common for samples destined for mass spectrometry since the silver staining impairs the analysis. After excision of the protein band of interest from the gel most protocols require a destaining of the proteins before proceeding. The destaining solution for CBB contains usually the buffer salt ammonium bicarbonate (NH4HCO3) and a fraction of 30%-50% organic solvent (mostly acetonitrile). The hydrophobic interactions between protein and CBB are reduced by the organic fraction of the solution. At the same time, the ionic part of the solution diminishes the electrostatic bonds between the dye and the positively charged amino acids of the protein. In contrast to a mixture of water with organic solvent the effectivity of destaining is increased. An increase of temperature promotes the destaining process. To a certain degree (< 10%) the destaining procedure is accompanied with a loss of protein. Furthermore, the removal of CBB does not affect the yield of peptides in the mass spectrometric measurement. In the case of silver stained protein bands the destaining is accomplished by oxidation of the metallic silver attached to the protein by potassium ferricyanide or hydrogen peroxide (H2O2). The released silver ions are complexed subsequently by sodium thiosulfate. The staining and destaining of gels is often followed by the reduction and alkylation (r&a) of the cystines or cysteines in the proteins. Hereby, the disulfide bonds of the proteins are irreversibly broken up and the optimal unfolding of the tertiary structure is obtained. The reduction to the thiol is accomplished by the reaction with chemicals containing sulfhydryl or phosphine groups such as dithiothreitol (DTT) or tris-2-carboxyethylphosphine hydrochloride (TCEP). In course of the subsequent irreversible alkylation of the SH groups with iodoacetamide the cysteines are transformed to the stable S-carboxyamidomethylcysteine (CAM; adduct: -CH2-CONH2). The molecular weight of the cysteine amino-acid residue is thereby increased from 103.01 Da to 160.03 Da. Reduction and alkylation of cysteine residues improves peptide yield and sequence coverage and the identification of proteins with a high number of disulfide bonds. Due to the rareness of the amino acid cysteine for most of the proteins the step of r&a does not effect any improvement of the mass spectrometric analysis. For the quantitative and homogeneous alkylation of cysteines the position of the modification step in the sample-preparation process is crucial. With denaturing electrophoresis it is strongly recommended to perform the reaction before the execution of the electrophoresis, since there are free acrylamide monomers in the gel able to modify cysteine residues irreversibly. The resulting acrylamide adducts have a molecular weight of 174.05 Da. Afterwards the eponymous step of the method is performed, the in-gel digestion of the proteins. By this procedure, the protein is cut enzymatically into a limited number of shorter fragments. These fragments are called peptides and allow for the identification of the protein with their characteristic mass and pattern. The serine protease trypsin is the most common enzyme used in protein analytics. Trypsin cuts the peptide bond specifically at the carboxyl end of the basic aminoacids arginine and lysine. If there is an acidic amino acid like aspartic acid or glutamic acid in direct neighborhood to the cutting site, the rate of hydrolysis is diminished, a proline C-terminal to the cutting site inhibits the hydrolysis completely. An undesirable side effect of the use of proteolytic enzymes is the self digestion of the protease. To avoid this, in the past Ca2+-ions were added to the digestion buffer. Nowadays most suppliers offer modified trypsin where selective methylation of the lysines limits the autolytic activity to the arginine cutting sites. Unmodified trypsin has its highest activity between 35 °C and 45 °C. After the modification, the optimal temperature is changed to the range of 50 °C to 55 °C. Other enzymes used for in-gel digestion are the endoproteases Lys-C, Glu-C, Asp-N and Lys-N. These proteases cut specifically at only one amino acid e.g. Asp-N cuts n-terminal of aspartic acid. Therefore a lower number of longer peptides is obtained.