High-Resolution Two-Dimensional Electrophoresis

Summary

Two-dimensional gel electrophoresis (2-DE) with immobilized pH gradients (IPGs) combined with protein identification by mass spectrometry is currently the workhorse for the majority of ongoing proteome projects. Although alternative/complementary technologies, such as MudPIT, ICAT, or protein arrays, have emerged recently, there is up to now no technology that matches 2-DE in its ability for routine parallel expression profiling of large sets of complex protein mixtures. 2-DE delivers a map of intact proteins, which reflects changes in protein expression level, isoforms, or post-translational modifications. High-resolution 2-DE can resolve up to 5,000 proteins simultaneously (∼2,000 proteins routinely), and detect and quantify <1 ng of protein per spot. Today’s 2-DE technology with IPGs has largely overcome the former limitations of carrier ampholyte-based 2-DE with respect to reproducibility, handling, resolution, and separation of very acidic or basic proteins. Current research to further advance 2-DE technology has focused on improved solubilization/separation of hydrophobic proteins, display of low abundance proteins, and reliable protein quantitation by fluorescent dye technologies. Here, we provide a comprehensive protocol of the current high-resolution 2-DE technology with IPGs for proteome analysis and describe in detail the individual steps of this technique, i.e., sample preparation and protein solubilization, isoelectric focusing in IPG strips, IPG strip equilibration, and casting and running of multiple SDS gels. Last but not the least, a section on how to circumvent the major pitfalls is included.