chapter  12
22 Pages

Statistical Methods for Classifying Mass Spectrometry Database Search Results

Proteomics, the large scale analysis of proteins, holds great promise to enhance our understanding of cellular biological process in normal and disease tissue [32]. The proteome is defined as the complete set of proteins expressed by a cell, tissue or organism. Transcript level analysis, as typically measured by DNA microarray technologies [35, 26], does not provide complete information on the proteome in that the DNA transcriptional template of an organism is static, whereas the proteome is constantly changing in response to environmental signals and stress. Recent studies have been unable to establish a consistent relationship between the transcriptome and proteome [3, 30]. The main reason is that transcript profiles do not provide any information on posttranslational modifications of proteins (such as phosphorylation and glycosylation) that are crucial for protein transport, localization and function. Studies have shown that the correlation between mRNA levels and protein abundance was poor for low expression proteins [17]. Posttranslational modifications such as glycosylation, phosphorylation, ubiquitination and proteolysis produce further modifications, which lead to changes in protein abundance.