Two-Dimensional Gel Electrophoresis as an Information Base for Human Proteome

Abstract

The main intricacy in the human proteome is that it is tremendously complex and com- posed of diverse and heterogeneous gene products. These products are called protein species or proteoforms and are the smallest units of the proteome. In pursuit of the comprehensive profiling of the human proteome, significant advances should be performed. The approaches that allow disclosing and keeping the information about human proteome using two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods such as mass spectrometry of high resolution and sensitiv- ity (MALDI-TOF MS and ESI LC-MS/MS) or immunodetection in combination with bioinformatics and 2DE can be used for the development of a comprehensive knowledge base of the human proteome. over 250 maps for 23 species, totalizing nearly 40,000 identified spots, making it the biggest gel-based proteomics dataset accessible from a single interface. Here, we can select a 2DE map which will be displayed for inspection. The database can be queried by keywords (protein description, protein name, gene name, species, author, full text, protein spot serial number) or graphically by clicking on a spot. Each spot is linked to a page containing the corresponding gene (protein) information and identification details. Also, information is displayed about other spots in different maps, where product of the same gene is detected. All these spots are highlighted in the maps and the calculated parameters [isoelectric point (pI) and molecular weight (Mw)] are displayed. There is a possibility for cross-references and obtaining more information from different 2DE databases and from UniProtKB. UniProtKB, a comprehensive protein sequence knowledge base has two sections: UniProtKB/Swiss-Prot, which is manually curated and UniProtKB/TrEMBL that contains computer-annotated entries. UniProtKB/Swiss-Prot entries provide users with cross-links to about 100 external databases and with access to additional information or tools [52].