A de novo peptide sequencing method and system based on hcd and etd mass spectrometry

Abstract

The present invention provides a peptide de novo sequencing method and system based on HCD and ETD mass spectrograms. The method includes: step 1, corresponding HCD and ETD mass spectrograms to form a new mass spectrogram, and pre-processing the new mass spectrogram. Processing, detecting effective spectral peaks and deleting interference spectral peaks; step 2, constructing a directed acyclic graph according to the effective spectral peaks; step 3, searching for a path that meets the weight rule in the directed acyclic graph, and according to The path generates candidate peptides; step 4, matching and scoring the candidate peptides with the new mass spectrum, sorting and outputting the candidate peptides according to the scoring results. The invention makes up for the shortcoming of incomplete spectral peaks caused by a single fragmentation type, combines the respective advantages of HCD and ETD spectral diagrams, and improves the accuracy of de novo sequencing. At the same time, preprocessing is performed before de novo sequencing to remove a large number of isotopic peaks and noise peaks to avoid interference with the de novo sequencing algorithm. And use a more discriminative scoring algorithm to improve the performance of 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