A de novo sequencing method

Abstract

The invention provides a de novo sequencing method which includes the steps: seeking a mirror image spectrogram corresponding to a mirror image peptide fragment in two data sets generated by enzyme digestion; detecting a high-reliability spectrum peak and a common spectrum peak from the mirror image spectrogram; building a directed acyclic graph according to the high-reliability spectrum peak andthe common spectrum peak; generating a candidate peptide fragment based on the built directed acyclic graph. A node corresponding to the high-reliability spectrum peak is a high-reliability node, anda node corresponding to the common spectrum peak is a common node. According to the method, mutual evidence is achieved by the aid of the mirror image spectrogram, and de novo sequencing accuracy of the peptide fragment can be improved.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a de novo sequencing method. Background technique [0002] Currently, protein identification methods based on mass spectrometry data fall into two categories: database searching and de novo peptide sequencing. Due to the continuous development and improvement of protein databases, database searching is the main method for identifying proteins. However, since the de novo sequencing method does not rely on the existing database, it can directly deduce the peptide sequence from the spectrum according to the characteristics of the regular fragmentation of the peptide, and has a database for identifying unknown proteins, post-translational modifications, and amino acid mutations. The irreplaceable advantage of the search method. [0003] Existing de novo sequencing methods are mainly divided into three categories: chemical labeling techniques, mass spectrometry techni...

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Problems solved by technology

[0004] However, there are two problems in the existing de novo sequencing method: 1) the ion fragmentation is incomplete, so that it is impossible to distinguish between AB and BA, resulting in a considerable number of spectra that cannot be obtained using the de novo sequencing method to obtain complete peptides; 2) the spectral peak The ion type of each peak is unknown, and it is generally believed that a peak can only match one type of ion. Therefore, when the ion type of the spectral peak is unknown, it is necessary to enumerate the ion type of each peak, which needs to be considered when calculating candidate peptides. Solve anti-symmetric constraints, which is an NP-hard problem

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