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Introduction

The proteome of a body fluid, biopsy sample, cell or tissue is the entire set of proteins that it contains. It is important to realize, however, that proteomes are highly dynamic and continually change in response to a variety of stimuli. The term 'proteome' was first used at a conference in Italy in 1994, the term 'proteomics' was introduced shortly after, and their importance in oncology was described in 2000.1–4 There has since been rapid progress in the technologies available to analyse and compare proteomes. It has been an active and moderately successful field for discovering protein biomarkers associated with cancers.5,6

It is also important to understand that the study of proteomes is far more complicated than the study of genomes. This is not just due to variations over time, but also because one gene can give rise to multiple different protein forms as a result of numerous post-translational modifications such as phosphorylation and ubiquitination, which can dramatically influence protein function. Given the large number of proteins, their multiple forms and wide dynamic range of concentrations, any study really only examines a proportion of the proteins present.

In oncology, a widely used approach has been to deploy proteomic technologies to analyse proteomes of cells or tissues in different states. Analysis commonly compares benign with malignant, malignancies with different degrees of differentiation, or malignancies with different clinical behaviours. Such comparisons are empirical and the differences derived have to be carefully validated to ensure that they are of biological and clinical significance. The topic is fast moving and the integration of proteomics with genomics represents a current, exciting and clinically relevant area of study.

Proteomic technologies

Proteomics depends on the deployment of high-quality, state-of-the-art technologies which require considerable investment in facilities and expert staff to generate results that are likely to be relevant to changing clinical practice. Consistently collected samples and associated clinical data are also an important component. Core approaches have included:

  • The separation of proteins on gels, usually relying on their mass and their charge and commonly in two dimensions. This technique was central to early studies in proteomics, but it is technically challenging, is labour intensive and has relatively low throughput; it has now largely been superseded by other technologies.

  • The separation and amino acid sequencing of component peptides formed from enzymatic digestion of the proteins present in a sample, using liquid chromatography-mass spectrometry. Rapid progress in mass spectrometry technology has allowed proteomic studies to be developed with high throughput, enabling several thousand proteins to be confidently identified in any given tissue with relatively simple sample preparation, and many more if more extensive sample fractionation is employed. Using appropriate statistics and bioinformatics, the outputs of such studies can include quantitative comparisons between proteomes, including direct identification of the proteins of interest (Figure 7.1). Importantly, the ability to examine the ...

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