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Proteomics is the study of protein structures and functions. Proteins can be chemically modified in different ways after synthesis and they are essential parts of living organisms. In Cancer Research, scientist believes that Proteomics is a fast growing science and it provides support in cancer diagnosis and further in treatment as well. Although, there are many known potential difficulties where the sensitivity, specificity, and reproducibility of the available molecular markers are unsatisfactory and do not match the expectations. But scientist still believe that with the improvement and advancement of proteomics technology, early diagnosis and treatment of cancer will be efficient and reliable in future. The human genome consists of complete set of genes that is required to build a functional human being. But the genome is just a source of information. In other words it is just a raw information and in order to function this information, it must be expressed in protein. The very first stage of gene expression is the transcription of genes and later it is followed by the translation of messenger RNA to actually produce proteins. The term proteome basically describes the entire set of proteins expressed by a given genome, cell, tissue, or organism at any one time. The complexity of proteome is much more higher than either the genome or the transcriptome. The reason of this is very simple, As each protein can be chemically modified in different ways after synthesis depending on its structrue and the way it folds. Most proteins have carbohydrate groups added to them. Some proteins have phosphorylated or acetylated or methylated groups added to them. The functions of the protein is totally dependent on the folded structure and the folded shape or structure of a proteins specified by its amino acid sequence. At cellular level, most of our cells have the same genome despite of the cell type, developmental stage or environmental conditions. But the proteome,being very dynamic, usually differs significantly in these differing circumstances and conditions. It can be due to different gene expression patterns or it can be different protein modification patterns.(1)
The study of proteom gives a better understanding of an organism than genomics. In a cell, proteins represent the actual functional molecules. The changes that happens at the DNA level, it affects the proteins. e.g. if mutations occur in the DNA, it is the proteins that are eventually affected. Same in case of Drugs, when they have favorable effects, they do so by having an interaction with proteins.(1)
Proteomics covers different aspects of protein function, It includes the following:
Structural proteomics, it includes the analysis of protein structures at large-scale. Where protein structure are compared and it helps to identify the functions of those genes which are newly discovered. The structural analysis also helps to understand that where drugs bind to proteins and also show where proteins interact with each other. This understanding is achieved using different technologies such as X-ray crystallography and NMR spectroscopy.(1)
Expression proteomics, includes the analysis of protein expression at larger scale. Where it helps to identify the main proteins that are found in a particular sample and those proteins which are differentially expressed in related samples, such as diseased vs healthy tissue. If a protein is found only in a diseased sample then it can be a useful drug target or diagnostic marker. Proteins with same or similar expression profiles may also be functionally related. There are technologies such as 2D-PAGE and mass spectrometry that are used in expression proteomics.(1)
Interaction proteomics, is the analysis of protein interactions at larger scale. The characterization of protein-protein interactions are useful to determine the protein functions and it also explains the way proteins assemble in bigger complexes. There are technologies such as affinity purification, mass spectrometry and the yeast two-hybrid system which are particularly useful in interaction proteomics.(1)
The proteome analysis techniques are not simple and straightforward as those which are used in transcriptomics. But the benefit of proteomics is that it deals with the real functional molecules of the cells. It is known that Strong gene expression results in an abundant mRNA but it does not necessarily mean that the corresponding protein is also abundant. In proteomics things are not so simple as one gene does not always produce the same protein. The genes usually consist of a series of sub structures, which are called exons. These sub structures can be joined in a variety of ways which helps to give momentum to whole series of very similar but different proteins. Further increasing complications, once proteins are made, they are ornamented with different other chemicals. These chemicals can be phosphate, sugars or fats. The affect of the decorations is so severe on the function of protein, for example phosphate normally behaves as an on-off switch and sugars usually tells the proteins where to go and attach in the cell. Therefore, it was comparitivly very simple and easy to sequence human genome as there are only 46 molecules and they are made up of 4 building blocks or letters (A,C,G,T) where as proteins have 20 building blocks and each of which can be customized or ornamented after the protein is built. Hence, proteome have to deal with ca. 30,000 genes which can be arranged to give some 800,000 proteins that can be modified and decorated with over 300 different chemicals. Additionally, proteomics also describe the nature of proteins, where they are being produced in a particular cell type and at a specific time. The way they are modified in the cell and the location where they are modified and also with whom they are in contact. Finally, the most difficult thing, is to determine the function of the protein.(1)