The challenge of proteomics

However, there are significant problems with using the combination of 2D electrophoresis and mass spectrometry. First, only the high abundance proteins are identified on 2D gels -it has been estimated that the number of genes expressed at any one time in a human cell type could exceed 10 000. If post-translational modification were also considered then the numbers of distinct polypeptides even within a single cell could run into the millions. On 

4 Deciphering protein networks by tandem affinity purification 

Oblain a list of pairs of interacting proteins from the libraTy 

Transcriptional activation only takes place when the two proteins are tethered to one another. Typically, the yeast protein GAL4 is used as the transcriptional activator together with the DNA binding domain of E. coli LexA as the other component. Two proteins can be probed for binding interactions with each other by fusing the activation domain to one protein and a complementary DNA binding domain to the second protein if the two proteins interact then a reporter gene will be transcribed by default. 

It has been estimated that 20-30 per cent of proteins encoded by the human genome are membrane proteins. Clearly, this makes membrane proteins a vital class to understand, and furthermore more than 70 per cent of drug targets are membrane proteins. A significant problem in mass spectrometry is that a far smaller number of membrane proteins are identified 

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It is interesting to note that the foremost challenges for the detailed modeling of the intact organism (computing time, complexity of interactions, model selection) are very similar to those entailed by the analysis of proteomic or genomic data. In the clinical case, complexity shifts from the richness of the data set to the model formulation, whereas in the proteomic-genomic case the main source of difficulties is the sheer size of the data set however, at least at present, interpretative tools are rather uncomplicated. 

From the anal5hical standpoint, large-scale, comprehensive analysis of proteins is an extremely challenging undertaking because of the enormous complexity of proteomes and their dynamic nature. In fact, the development of proteomics as a... 

A key related property of carbohydrates in their role as mediators of cellular interactions is the tremendous structural diversity possible within this class of molecules. Carbohydrates are built from monosaccharides, small molecules that typically contain from three to nine carbon atoms and vary in size and in the stereochemical configuration at one or more carbon centers. These monosaccharides may be linked together to form a large variety of oligosaccharide structures. The unraveling of these oligosaccharide structures, the discovery of their placement at specific sites within proteins, and the determination of their function are tremendous challenges in the field of proteomics. 

The challenges for proteome studies are many. The sensitivity of protein identification must be increased by a factor of 100 to 1000. In addition, systems must automatically detect protein concentrations over a 10,000-fold range, determine and rank protein changes between two or more samples, and identify change signatures. 

We see two major appearing frontiers for new kinds of molecular data. The first is proteomics (See Chapter 4 of volume 2) and metabolomics. With a combination of 2D gel, mass spectrometry, protein microarray and yeast-two-hybrid methods, a large amount of protein sequence, expression, and interaction data will be produced on a cell-wide level. On the one hand, bioinformatics has to address the challenge of interpreting these data. On the other hand, especially the protein interaction data will provide an interesting basis for probing deeper into the details of regulatory networks. Such data are collected in special protein interaction databases such as DIP [9,10] and BIND [11],... 

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