Proteomics and Bioinformatics

Abstract

The chapter focuses on the use of existing bioinformatics approaches in the analysis of global-protein expression using two-dimensional electrophoresis and mass spectrometry and on the extension of bioinformatics to include the analysis and management of the proteome data being produced. Bioinformatics will, of necessity, come to include the acquisition, analysis, and management of such protein-expression data, as well as the integration of those data with genome and protein sequence databases. The chapter discusses several bioinformatics tools, such as (1) sequence databases, (2) sequence analysis, and (3) annotation and proteomics tools—such as open reading frame (ORF) databases and proteomics, proteome (2DE) databases, and database integration. In the context of protein expression, the ORF sequences are used to select specific nucleotide sequences to include on the complementary DNA (cDNA) microarray chips used to quantify changes in specific messenger RNA (mRNA) abundance. The ORF sequences are also used as the starting material for protein arrays, providing the nucleic acid sequence that is incorporated into host cells to produce overexpression of the target proteins for the arrays. A comparative analysis of the metabolic processes of whole cells will be facilitated through the comparison of protein expression and genome sequence data from diverse cell types and the dream of computational cell modeling. Fully, and even partially, annotated genome databases have multiple uses in the broad context of proteomics, including protein structure and function prediction, as well as protein-expression analysis.