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Preliminary Search Engine for Open Protein Identification

Protein identification is the most important and basic problem for proteomics. Using tandem mass spectrometry and database search is one of the most widely used identification techniques. However, the improved sensitivity of mass spectrometers, rapid expansion of databases and more complex analysis, like post-translational modification and non-specific enzymatic digestion, have challenged current restricted protein identification search engines in scale and speed severely. In this paper, we proposed an open protein identification method relaxing enzyme, and presented our distributed design to support big protein database with non-specific digestion analysis based on pFind, a practical tandem mass spectra search engine developed in China. With classical bigger protein databases ipi. HUMAN and uniprot-sprot we got nearly linear speedup in a 20-blade cluster. By further analysis, we can expect real time identification to some extent.