Protein identification method and system

Abstract

The invention belongs to the technical field of biological analysis and in particular discloses a protein identification method and a protein identification system. The protein identification method comprises the following steps: performing digestion operation on protein to be tested according to protease, and acquiring a secondary mass spectrum of the protein to be tested by using a protein tandem mass spectrum technique; performing virtual digestion operation on a protein sequence in a protein database, and extracting a first type of peptide fragments meeting requirements; generating a theoretic spectrum by using an FPGA (Field Programmable Gate Array) according to the first type of the peptide fragments; comparing the secondary mass spectrum of the protein to be tested with the theoretic spectrum by using an FPGA acceleration module, and performing similarity scoring; confirming a peptide fragment corresponding to a theoretic spectrum with a highest score as a peptide fragment of the protein; and sequentially confirming all peptide fragment sequences of the protein, thereby obtaining protein sequences. By adopting the protein identification method and the protein identificationsystem disclosed by the invention, acceleration on the FPGA is achieved, the whole scoring process is accelerated for about 25 times, a good acceleration effect is achieved, and the operation efficiency of the system is improved.

Description

technical field [0001] The invention belongs to the technical field of biological analysis, and in particular relates to a protein identification method and system. Background technique [0002] Protein sequence identification is an important branch of biological sequence analysis technology. Today, among numerous protein identification algorithms, MS / MS technology, known for its accuracy, is a fast and reliable method that can handle large-scale data. Protein Identification Technology. [0003] The algorithm based on protein database query is one of the most widely used and more accurate techniques in peptide sequence identification algorithms, X! Tandem software uses the database query algorithm. The core of the protein peptide sequence recognition process based on the database query method is to generate a theoretical spectrum based on the known protein library, and then compare it with the MS / MS spectrum of the protein sequence to be tested to complete the similarity s...

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Problems solved by technology

But through X! The process of protein identification by Tandem software takes a long time and the operation efficiency is low

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