Method and system for accelerating large-scale protein identification by using suffix array

Abstract

The invention discloses a method and a system for accelerating large-scale protein identification by using a suffix array. The method comprises the steps of: 1, establishing a corresponding suffix array according to a protein sequence in a database, and deducing a longest public prefix corresponding to the protein sequence according to the suffix array; 2, performing online enzyme digestion on the protein sequence based on the longest public prefix and an enzyme digestion rule so as to obtain a non-redundant peptide; and 3, performing peptide mapping matching identification according to a tandem mass spectrum and the non-redundant peptide, and deducing a corresponding protein sequence by utilizing the peptide obtained through identification. According to the invention, the purposes of redundant peptide removal and rapid query are achieved, and the identification speed for the protein is increased; meanwhile, the method is beneficial to lossless precision, requires less time and space and is more convenient to use.

Description

technical field [0001] The invention relates to protein identification technology, in particular to a method and system for accelerating large-scale protein identification by using suffix array (SA, SuffixArray). Background technique [0002] Protein identification based on tandem mass spectrometry has become the mainstream technology of proteomics. Reference 1 "Aebersold, R. and Mann, M. Mass spectrometry-based proteomics, Nature, 2003, 422: 198-207" has a more detailed description . And database search has become the mainstream technology for identification of tandem mass spectrometry data, reference 2 "Eng, J.K., McCormack, A.L. and Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in aprotein database. J Am Soc Mass Spectrom , 1994, 5:976-989"; Reference 3 "Perkins, D.N., Pappin, D.J., Creasy, D.M.and Cottrell, J.S. Probability-basedprotein identification by searching sequence databases using mass spectrometrydata. "; ...

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Problems solved by technology

[0007] The purpose of the present invention is to provide a method and system for accelerating large-scale protein identification using suffix arrays, which are used to solve the slow speed of database search based on tandem mass spectrometry in current large-scale protein identification and the need for widely used inverted index creation The time and space are too large and inconvenient to use

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