PROTEOMICS PROTEIN SEQUENCE ANALYSIS

Proteomics is concerned with the analysis of the complete protein complements of genomes. Thus proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and functions. This chapter focuses on protein sequences as the sources of biochemical information. Protein sequence databases are surveyed. Similarity search and sequence alignments using the Internet resources are described. 

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Besides sensitive methods for the analysis of proteins, bioinformatics is one of the key components of proteome research. This includes software to monitor and quantify the separation of complex samples, e.g., to analyze 2DE images. Web-based database search engines are available to compare experimentally measured peptide masses or sequence ions of protein digests with theoretical values of peptides derived from protein sequences. Websites for database searching with mass spectrometric data may be found at http //www.expasy.ch/tools, http //prospector.ucsf. edu/ and http //www.matrixscience.com. 

Site offers mMass program that is an open source package of simple tools, written mainly in Phyton and dedicated to mass spectrometric data analysis. It can also be used for protein sequence handling and other proteomic tasks. 

Proteomics server of the Swiss institute of bioinformatics. Dedicated to analysis of protein sequences and structure, as well as 2-D SDS-PAGE. 

The limitations of genomic analysis are being addressed by proteomic analysis. DNA sequence analysis has helped to create protein product libraries and relational databases that hold promise to... 

The terms proteomics and proteome were coined by Wilkins et al. in 1994 to describe the entire collection of proteins encoded by genomes in the human organism. Proteomics differs from protein chemistry at this point since it focuses on multiprotein systems rather than individual proteins and uses partial sequence analysis with the aid of databases. Proteins are the bricks and mortar of the cells, carrying out most of the cellular functions essential for survival of the organism. In the cell, proteins... 

Currently available MS instruments are much more suitable for peptide analysis and the data obtained can be directly used for comparison with protein sequences derived from proteome databases. 

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