Proteomic Analysis of the Mammalian Cell Nucleus

This chapter discusses the proteomic analysis study of the mammalian cell nucleus. The proteome consists of all proteins present in a cell or organism at a given time, including not only those translated directly from genetic material, but also the variety of modified proteins arising from events, such as alternative splicing of transcripts and extensive posttranslational processing. Proteomics provides valuable information and correlates genome sequence information and the cellular behavior at the molecular level. In this chapter, approaches to perform proteomics of the mammalian cell nucleus are discussed. Major steps involve separation and identification of nuclear proteins using two-dimensional gel electrophoresis (2DE) and mass spectrometry (MS) followed by data analysis and interpretation using advanced bioinformatic techniques. Nuclear protein solubilization for sample preparation, isoelectric focusing of protein, concepts related to visualization of protein spots by staining 2D gels, details of coomassie brilliant blue R-250 staining, sypro ruby protein gel stain (Bio-Rad), and mass spectrometry compatible silver staining, andAn image analysis of two-dimensional gels are described.