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encompasses the <strong>in</strong>vestigation of prote<strong>in</strong>-prote<strong>in</strong> <strong>in</strong>teractions, the connection between<br />

the structure of prote<strong>in</strong>s and their function, cellular processes and networks, and to<br />

improve prote<strong>in</strong> separation and prote<strong>in</strong> profil<strong>in</strong>g techniques.<br />

The general workflow (Figure 2.2) <strong>in</strong> a 2D gel-based proteomics experiment and<br />

some of the factors affect<strong>in</strong>g the way the experiment is performed are outl<strong>in</strong>ed below.<br />

Figure 2.2. Schematic of workflow <strong>in</strong>volved <strong>in</strong> a proteomics experiment, Bio-rad.<br />

2.1.1. Prote<strong>in</strong> Profil<strong>in</strong>g and its Importance<br />

Prote<strong>in</strong> profil<strong>in</strong>g, an emerg<strong>in</strong>g <strong>in</strong>dependent subspecialty of proteomics, is poised<br />

to provide unprecedented <strong>in</strong>sight <strong>in</strong>to biological events. Quantitative evaluation of<br />

prote<strong>in</strong> levels can be accomplished with prote<strong>in</strong> profil<strong>in</strong>g, which shows us unique<br />

expression patterns (diseased vs. healthy, treated vs. untreated, experimental vs. control)<br />

at the prote<strong>in</strong> level when prote<strong>in</strong>s from one cell type are compared with those of another<br />

cell type. The value of prote<strong>in</strong> profil<strong>in</strong>g is <strong>in</strong>creas<strong>in</strong>g daily and there are several reasons<br />

why it is of great importance, especially as a potential tool for the early diagnosis of<br />

leukemias and other diseases.<br />

One such reason is that it provides a much better understand<strong>in</strong>g of an organism,<br />

as it is not always possible or sufficient for scientists to clarify some metabolic<br />

pathways, <strong>in</strong>clud<strong>in</strong>g mechanisms of diseases, exclusively by study<strong>in</strong>g the genome<br />

(Graves and Haystead, 2002). Additionally, there are some difficulties associated with<br />

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