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Protein secondary mass spectrum identification method of marker loci based on candidate peptide fragment discrimination

A technology of labeling spectra and secondary mass spectrometry, which is applied in the field of protein secondary mass spectrometry identification, can solve the problems of insufficient comprehensiveness and little consideration of continuous peak matching, etc.

Inactive Publication Date: 2013-08-14
JINAN UNIVERSITY
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

These statistical model-based algorithms mainly consider the matching and mismatching of experimental mass spectrum peaks, and seldom consider the continuous matching of peaks or consider them comprehensively enough.

Method used

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  • Protein secondary mass spectrum identification method of marker loci based on candidate peptide fragment discrimination
  • Protein secondary mass spectrum identification method of marker loci based on candidate peptide fragment discrimination
  • Protein secondary mass spectrum identification method of marker loci based on candidate peptide fragment discrimination

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0073] Virtually digest the protein database sequence, and establish a peptide database and a peptide database index for the peptide after enzymatic digestion according to the mass number of the peptide. The steps are as follows:

[0074] (1) Read a protein sequence in the species protein sequence library file of the mass spectrometry sample (that is, the sample to be analyzed by MS / MS).

[0075] (2) Carry out virtual theoretical digestion of the protein sequence according to Table 1 according to the protease set by the user and the number of allowed missed cleavage sites. At present, most trypsin is used for protein enzymatic hydrolysis experiments. It can be seen from Table 1 that Trypsin is sensitive to protein C-Term, that is to say, an amino acid may be cut off at the C-terminus of the protein sequence; its enzyme cleavage site KR, that is to say The enzyme cuts on the K and R of the sequence; its restriction enzyme cut site is P, that is to say, when the restriction enzy...

Embodiment 2

[0101] According to the mass-to-charge ratio peptide database of the parent ion in the experimental spectrum to be analyzed (secondary mass spectrometry), find out the candidate peptides that meet the requirements, and generate theoretical spectra that meet the requirements for all the candidate peptides found.

[0102] (1) According to the parent-child mass-to-charge ratio of the secondary mass spectrum to be analyzed, the method of finding the candidate peptides that meet the requirements:

[0103] 1) Load the database.index file information to the memory array index, read the m / z value and charge (charge) information of the parent ion of the secondary mass spectrometer to be analyzed, and calculate the mass number of the parent ion after it is decharged, for example, there is a m / z=2100.2, charge=2 parent ion information, its mass number after decharge is m / z*2-2=4198.2.

[0104] 2) Find the index array record and read the corresponding peptide information according to the ...

Embodiment 3

[0114] The steps of de-isotope peak processing and selection of effective peaks for the experimental spectrum to be analyzed are as follows:

[0115] (1) Deisotope peak

[0116] Theoretically, the mass-to-charge ratio m / z difference between isotopic peaks is 1 and the peak intensity between isotopic peaks is controlled by the natural isotopic abundance. For example, the abundance of C12 in nature is higher than that of C13, and the height of its mass spectrum peak is also higher than that of C13. Among the stable isotopes in nature, the basic abundance of low molecular weight accounts for the highest abundance. In a mass spectrum, in an isotopic peak group, the first peak should basically be the highest peak. In the measurement of the actual mass spectrometer, there are measurement errors in the mass spectrometer. Depending on the type of mass spectrometer, the measurement accuracy is also different. For example, the measurement error of LTQ mass spectrometer is 0.5Da. Sinc...

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Abstract

The invention discloses a protein secondary mass spectrum identification method of marker loci based on candidate peptide fragment discrimination, and relates to the field of protein secondary mass spectrum identification. The method comprises the following steps of: establishing a peptide fragment database and a peptide fragment database index; finding out candidate peptide fragments from the peptide fragment database according to parent ions in a to-be-analyzed experiment loci, and generating a theory loci; removing isotopic peaks and selecting effective peaks from the to-be-analyzed experiment loci; generating an experiment marker loci based on candidate peptide fragment discrimination; counting peak intensity discrimination of different sections, theory fragment ions and experiment loci quality error discrimination and fragment ion discrimination of experiment loci peaks and theory loci matching peaks; marking discrimination of each candidate peptide fragment based on the experiment loci matching ions, and selecting the peptide fragment with the highest score as the identification result of the experiment loci. The method is higher in quantity of identified effective mass spectra and quantity of identified protein peptide fragments than the existing algorithm, so that the identification efficiency is also greatly improved.

Description

technical field [0001] The invention relates to the field of protein secondary mass spectrometry identification, in particular to a protein secondary mass spectrometry identification method based on a candidate peptide segment discrimination marker map. Background technique [0002] Biomass spectrometry has become one of the supporting technologies for proteome research, which mainly uses tandem mass spectrometry (LC-MS / MS) to analyze protein samples. In the bioinformatics research of proteome, MS / MS data processing is a very important research content, and its task is to infer the protein composition of the sample from the data with noise or partial information missing. Database search is the main method of mass spectrometry data processing, and its basic process is as follows: figure 1 Shown: compare and score the experimental map and the theoretical restriction map in the database, and select the match with the highest score as the candidate peptide of the search result....

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N27/62
Inventor 肖传乐杜阳利陈晓舟何庆瑜
Owner JINAN UNIVERSITY
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