Theoretical Proteomics - from protein identification to biological evolution
S. June Oh
College of Medicine, Inje University
2009. 2. 6
301-421, 13:30 PM
tsORFdb and massProphet: Almost all peptide mass fingerprinting (PMF) tools employ only known or predicted protein sequences and do not include open reading frames (ORFs) in the genome, which eliminates the chance of finding novel functional peptides. Unlike most tools that search protein sequences from known coding sequences, the tool uses a database for theoretical small ORFs (tsORFs) and a PMF application using a tsORFs database (tsORFdb). The tsORFdb is a database for ORFeome that encompasses all potential tsORFs derived from whole genome sequences as well as the predicted ones. The massProphet system tries to extend the search scope to include the ORFeome using the tsORFdb.
Membrane proteins of a cell play crucial roles in the cell's interaction with its environment and whitin itself. They consist of membrane-bound proteins and many types of transmembrane (TM) proteins such as receptors, transporters, channel proteins, enzymes, and other functional proteins. Membrane proteomes of cellular organisms reveal some characteristics in global topological distribution according to their evolutionary positions to show their own information transfer complexity. Transmembrane characteristics of cellular membrane proteome reaffirmed the important roles of membrane receptors in cellular communication and biological evolutionary history.
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