Topological proteomics

ExPASy Proteomics tools (http //expasy.org/tools/), tools and online programs for protein identification and characterization, similarity searches, pattern and profile searches, posttranslational modification prediction, topology prediction, primary structure analysis, or secondary and tertiary structure prediction. 

Schubert, W. (2003). Topological proteomics, toponomics, MELK-technology. Advances in Biochemical Engineering/Biotechnology, 83, 189-209. 

Topological proteomics means visualization of the abnormal cellular protein networks, cell by cell. Conventional proteomics is performed in three steps separation of complex protein mixtures, characterization of the separated proteins, and database searching to identify the composition of the complex. The employed techniques such as 2-D electrophoresis and mass spectrometry use tissue homogenates. Therefore, only quantitative changes of the most abundant proteins with particular biochemical properties can be detected. Any topological information, information on the cellular and sub-cellular distribution of proteins, that determines protein-interactions in networks, is lost. 

Kim H, Melen K, Osterherg M, von Heijne G (2006) A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc Natl Acad Sci USA 103 11142-11147... 

Another possible parameter for correlation that would increase validity is the localization and topology of a suspected biomarker within the tissue, and this is why biomarker discovery-in combination with molecular imaging-is attracting interest at such a rapid pace. It must be borne in mind, however, that even a reasonable locaHzation pattern of a low-resolution mass spectrometric signal is stiU not sufficient proof of the presence of an expected substance that has been identified beforehand from a bulk proteomics experiment. 

The introduction of two dimensional (2D) graphs and their numerical characterization for comparative analyses of DNA/RNA and protein sequences without the need of sequence alignment is an active yet recent research topic in bioinformatics. Here we used a 2D artificial representation (four color maps) with a simple numerical characterization through topological indices (TIs) to aid the discovering of remote homologous of Adenylation domains (A-domains) from the Nonribosomal Peptide Synthetases (NRPS) class in the proteome of the cyanobacteria Microcystis aeruginosa. 

---