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 2-DE is a classical method to separate intact proteins and semi-quantify proteins with good abundance; it is especially useful in the study of protein modifications. 2-DE is usually used to find biomarkers in various disease states. We have several 2-DE systems purchased from GE and Bio-Rad. The high throughput, quality and reproducibility enabled by 2-DE gels are well reproduced in our facility. Of note, sample preparation is the most important part in this method. We have successfully extracted proteins for 2-DE run from a diversity of samples such as cell membrane, cell wall, cell organelles, cells, tissues, organs, body fluids, plant leaf, stem, ear and root. DIGE system is a fully integrated system offering significant benefits over classical 2-D electrophoresis. 2-D fluorescence difference gel electrophoresis ensures that each protein spot has its own internal standard. It is an effective way to remove gel to gel variation, thereby significantly increasing accuracy and reproducibility. We have successfully developed the Ettan DIGE system in our lab and analyze the spot difference from several types of samples by this method. The other gel-based techniques, such as 1-D-PAGE and 1-D-IEF, can provide a more sensitive strategy to characterize and identify proteins together with LC-MS. These methods are often used to profile the proteomes of samples or perform specific difference analysis.
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