Gene Expression Profiling

Volume 784 of the series Methods in Molecular Biology pp 123-137


2D Gel Electrophoresis and Mass Spectrometry Identification and Analysis of Proteins

  • Paula MeleadyAffiliated withNational Institute for Cellular Biotechnology, Dublin City University Email author 

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Analysis of the protein expression patterns in clinical samples and cells by proteomic technologies offers opportunities to discover potentially new biomarkers for early detection and diagnosis of disease. One of the most widely used techniques to study the proteome of a biological system is two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). In particular, a modified version of 2D-PAGE, two-dimensional difference gel electrophoresis (2D-DIGE), which uses differential labelling of protein samples with up to three fluorescent tags, offers greater sensitivity and reproducibility over conventional 2D-PAGE. In this chapter, we will introduce methods for the analysis of whole cell lysates from human cancer cell lines using 2D-DIGE and identification of differentially expressed proteins using liquid chromatography mass spectrometry, i.e. LC–MS/MS.

Key words

Two-dimensional gel electrophoresis Two-dimensional difference gel electrophoresis Mass spectrometry Protein expression profiling Proteomics