Proteome databases

Field, H.I., Fenyo, D., Beavis, R.C. (2002). RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database. Proteomics 2, 36 17. 

H. I. Field, D. Fenyo, and R. C. Beavis. RADARS, a Bioinformatics Solution that Automates Proteome Mass Spectral Analysis, Optimises Protein Identification, and Archives Data in a Relational Database. Proteomics, 2, no. 1 (2002) 36-47. 

The study of cellular protein expression by proteomics has relied on technologies that first appeared in the 1970s and have been continuously improved. In combination with advanced bioinformatics and large databases, proteomics now provide a powerful tool for basic research, clinical diagnostics, and drug development applications. 

Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, et al. Overview of the HUPO plasma proteome project Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005 5(13) 3226-3245. 

Xu, B., etal. (2005). Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database. Proteomics 5, 1083-1096. 

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. 

D) polyacrylamide gels. These types of experiments have been performed for more than twenty years to build databases of proteins expressed from certain cell or tissue types (Anderson and Anderson, 1996 O Farrell, 1975). Although this remains an important component of proteomics research, the field has expanded due to the development of additional technologies. Proteomics can be broadly divided into two areas of research (i) protein expression mapping, and (ii) protein interaction mapping. 

Pineda, F. J. Lin, J. S. Fenselau, C. Dimerov, P. A. Testing the significance of microorganism identification by mass spectrometry and proteome database search. Anal. Chem. 2000, 72, 3739-3744. 

The use of proteomics exploits one of the fastest-growing analytical technologies, with scientists worldwide contributing to the protein/genome databases, and to improved algorithms to search databases and identify proteins. 

Proteomics algorithms have been developed to search databases of protein sequences for matches to short sequences determined experimentally from proteins or peptides in the laboratory,5 59 and for theoretical matches to... 

Dworzanski, J. R Snyder, A. P. Chen, R. Zhang, H. Wishart, D. Li, L. Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring. Anal. Chem. 2004,76,2355-2366. 

An important issue in 2D liquid separations is finding a first dimension, which can provide information on the p7 of the protein. This is important as p7 information has biological significance in proteomics where it is a physical property listed in the databases and can aid in protein identification. The use of p7... 

Cargile, B.J., Bundy, J.L., Stephenson, JL., Jr. (2004). Potential for false positive identifications from large databases through tandem mass spectrometry. J. Proteome Res. 3, 1082-1085. 

Simpson RJ et al. Proteomic analysis of the human colon carcinoma cell line (LIM 1215] development of a membrane protein database. Electrophoresis 2000 21 1707-1732. 

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