An Iterative Search Algorithm for Protein Identification from Complex Patterns of Post-translational Modifications

摘要

Post-translational modifications (PTMs) of proteins are of extreme biological importance. As many as 300 PTMs are known to occur physiologically. Mass spectrometry (MS) is currently a central technology for identifying proteins with complex patterns of PTMs. Identification of PTMs is challenging for the conventional database matching algorithms because the number of candidates which must be tested expands exponentially as the number of modifications increases. De novo sequencing algorithms have been described in the literature as alternative approaches to this problem. However, performance of these methods is highly dependent on the complexity of sample and the quality of MS/MS spectra. We have developed an iterative search algorithm, termed ISPTM, using the OMSSA database search engine for identification of PTMs. This strategy was used to analyze PTMs from complex nuclear matrix (NM) proteins.