Method and system based on HCD mass spectrogram and ETD mass spectrogram for peptide fragment de novo sequencing

Abstract

The invention provides a method and a system based on an HCD mass spectrogram and an ETD mass spectrogram for peptide fragment de novo sequencing. The method includes steps of: (1) homologizing the HCD mass spectrogram and the ETD mass spectrogram to form a new mass spectrum, pretreating the new mass spectrum, detecting effective spectral peaks and deleting interference peaks; (2) constructing a directed acyclic graph according to the effective spectral peaks; (3) searching a route conforming the weight roles in the directed acyclic graph, and generating candidate peptide fragments according to the route; and (4) matching the candidate peptide fragments and the new mass spectrum, grading, sequencing the candidate peptide fragments according to the grading results, and outputting. The method and the system overcome disadvantages of defective spectral peaks caused by single fracture types, combine advantages of the HCD mass spectrogram and the ETD mass spectrogram, and increase the accuracy of the de novo sequencing. Pretreatment is performed before de novo sequencing to remove many isotope spectral peaks and noise spectral peaks, thus preventing the isotope spectral peaks and the noise spectral peaks from interfering the de novo sequencing algorithm. A grading algorithm with a high distinction degree is adopted, thus improving the performance of the de novo sequencing.

Description

technical field [0001] The invention relates to the field of biological information, in particular to a peptide de novo sequencing method and system based on HCD and ETD mass spectrograms. Background technique [0002] Peptide and protein identification using tandem mass spectrometry has become the core technology of current proteomics. Currently, there are two main technical routes for protein identification based on tandem mass spectrometry: database searching and de novo peptide sequencing. Due to the rapid development and improvement of protein databases, database search has become the main technology for protein identification. However, the de novo sequencing method does not rely on the existing database. According to the characteristics of the regular fragmentation of the peptide, the sequence of the peptide is directly deduced from the map, which can analyze the tandem mass spectrometry data of new species or species whose genome has not been sequenced, and has datab...

AI Technical Summary

Problems solved by technology

[0003] However, the peptide de novo sequencing method is not as widely used as the database search method. There are two main reasons: (1) The fragmentation information of the mass spectrum is incomplete, and quite a few spectra cannot be obtained using the de novo sequencing method. There are too many amino acids without fragmentation information; (2) The de novo sequencing method is equivalent to searching for the correct peptide in all amino acid combinations that meet the mass error range of the parent ion, and the search space is large, so that the calculation speed is very slow

In addition, it is generally believed that a spectral peak can only match one type of ion, so searching for a path in a mass spectrum needs to consider antisymmetric constraints, and searching for an antisymmetric path in a directed acyclic graph is an NP-hard problem

Images