Strategies for proteomics sample preparation

Two-dimensional (2-D) gel electrophoresis is a popular and proven separation technique for proteome analysis. The 2-D procedure is straightforward: Proteins are first separated according to their isoelectric point (pI) by isoelectric focusing (IEF) and then by their molecular weight by SDS-PAGE. For most researchers, 2-D gel electrophoresis is easy to learn, because advances in immobilized pH gradient (IPG) technology have eliminated the need for tricky and tedious IEF in ampholyte gel gradients. Nevertheless, problems with smearing, streaking, and poor resolution and reproducibility tend to leave researchers dissatisfied with the results of 2-D experiments. These common compalints are often due to improper sample preparation.

One of teh most undervalued aspects of the 2-D process, sample preparation prior to the first-dimension IEF separation contributes significantly to the overall reproducibility and accuracy of protein expression analysis. Some important considerations include:

  • Care must be taken to prevent protolysis during protein extraction, and proteins must be solubilized in a buffer that is compatible with IEF
  • Contaminants such as salts and detergents must be removed to ensure successful separation
  • Fractionation is essential to reduce protein sample complexity when analysis of subpopulations or low-abundance proteins is required

Without proper sample preparation, protein precipitations, gel streaking, and overall poor resolution are often the unfortunate result.

Click on this link to learn some great strategies for proteomic sample preparation.

Click to learn about Bio-Rad’s new Protean i12 IEF Cell.

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