Protein/peptide analysis development

How have neural networks been used in genome informatics applications In Part II, we have summarized them based on the types of applications for DNA sequence analysis, protein structure prediction and protein sequence analysis. Indeed, the development of neural network applications over the years has resulted in many successful and widely used systems. Current state-of-the-art systems include those for gene recognition, secondary structure prediction, protein classification, signal peptide recognition, and peptide design, to name just a few. 

Lue, R. Y, Zhu, Q., Li, D. (2004). Site-specific peptide immobilization strategies for the rapid detection of kinase activity on microarrays. Site-specific immobilization of biotinylated proteins for protein microarray analysis. Enzymatic profiling system in a small-molecule microarray. Intein-mediated biotinylation of proteins and its application in a protein microarray. Developing site-specific immobilization strategies of peptides in a microarray. Methods Mol. Biol. 278, 191-204. 

Another important development in the field of biopolymer analysis is the introduction of matrix-assisted laser desorption ionization (MALDl), which is a rather recent soft ionization technique that produces molecular ions of large organic molecules. In combination with time-of-flight (TOP) mass spectrometry, it was proposed as a valuable tool for the detection and characterization of biopolymers, such as proteins, peptides, and oligosaccharides, in many types of samples.The use of these recently developed techniques has not decreased the use of chromatography in determinations of biopolymers. Some efforts on the adaptation of the separation abilities of HPLC to the high potential of MALDl-TOF for the sensitive determination of additives in biocomposites are currently being carried out. 

The application area of LC-MS is rapidly growing. LC-MS is now regularly used for the analysis of many different types of compound drugs and metabolites, herbicides-pesticides and metabolites, surfactants, dyes, saccharides, lipids-phospholipids, steroids, and many others. In our opinion, the area that profits more from the development of LC-MS is bioanalysis natural products, proteins, peptides, nucleosides, and metabolic studies. Despite the current trends toward immunoassays-biospecific assays and capillary electrophoresis, LC-MS is an extremely powerful analytical technique that is considered complementary to the above mentioned, rather than competitive. 

Unlike mammalian cells, which cannot synthesize all amino acids, SILAC is not well suited to studying the protein/peptide levels of microorganisms, most of which are prototrophic for all amino acids. Application of SILAC in such cases is mostly restricted to auxotrophic strains, which renders the technique ineffective for the proteome analysis of many commercially important microbes. Native SILAC (nSILAC), a recently developed modification of... 

This chapter reviews the current state of the art in the design and fabrication aspects of microfabricated electrophoresis devices, as well as the development of popular detection modes applicable to microchip devices. Potential applications in the pharmaceutical industry are highlighted based on the successful analysis of proteins, peptides, DNA, chiral separations, and some small molecules. 

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