Protein/genome databases

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. 

These classical bioinformatics strategies are not all directly applicable to analysis of intact microorganisms, which each contain a mixture of protein biomarkers. Flowever, the principle of comparing experimental observations to protein/genome databases (bioinformatics) does hold the key to flexibility,... 

Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendra-nath V, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003 13 2363-71. 

MS instruments measure the mass-to-charge ratio (m/z) values of the smallest of molecules very accurately. In addition, the development of translated genomic databases and specialized software algorithms that rapidly search MS data against theoretical spectra of known or predicted proteins within databases is an important component that greatly facilitated the emergence of mass spectrometry-based proteomics as a key approach for large-scale proteomic analysis.15... 

Other databases, including DNA and protein databases, the Human Genome Database (GDB), and Medline. Two relatively new query systems in OMIM, OMIM Gene Map and OMDVt Morbid Map, provide cytogenetic map locations of diseases and gene lists organized by diseases, respectively. 

Peri, S., Navarro, J.D., Amanchy, R., Kristiansen, T.Z., Jonnalagadda, C.K., Suren-dranath, V., Niranjan, V., Muthusamy, B., Gandhi, T.K., Gronborg, M., et al, (2003) Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans. Genome Res, 13,2363-2371. 

If PMF and sequence homology searches fail using available protein and EST databases, mass spectrum data can, in principle, be used to search genome databases (GenBank http //www.ncbi.nlm.nih.gov/). However, only a small percentage of large genomic sequences code for proteins such that bioinformatics still needs to accurately define exon-intron structures (Andersen and Mann, 2000). 

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