A database search algorithm based on information theory for protein identification

The ITPIA (information theory based protein identification algorithm) based on information theory is proposed to search protein database by use of polypeptide tandem mass spectra for more exact protein identification. To solve efficiently the problem of low-quality and noisy spectra, the entropy theory is introduced in the ITPIA with a scoring system built to measure the similarity between the experimental spectrum and the theoretical spectrum of polypeptide in the database. The algorithm thus acquires more information on protein structure via the polypeptide tandem mass spectra. Experimental results showed that ITPIA algorithm can effectively improve the exactness of protein identification.