Method of identifying protein phosphorylation modification sites on the basis of tandem mass spectrometry

A tandem mass spectrometry and phosphorylation technology, which is applied in the field of identification of protein phosphorylation modification sites based on tandem mass spectrometry, can solve the problem of high limitations, and achieve the effect of accurate identification and improved reliability.

Inactive Publication Date: 2013-08-28
INST OF AQUATIC LIFE ACAD SINICA
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Currently, software for protein phosphorylation site modification site evaluation includes PTMScore, Ascore, and PhosphoRS in MaxQuant, but these software have relatively high limitations and are only applicable to data generated by specific mass spectrometry instruments and specific database search programs, such as PTMScore and PhosphoRS in MaxQuant are only used for a series of mass spectrometers from Thermo, and Ascore is only compatible with the search results of the Sequest database; in addition, based on the PTMScore algorithm in Max

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  • Method of identifying protein phosphorylation modification sites on the basis of tandem mass spectrometry

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Embodiment 1

[0030] Example 1: Identification of protein phosphorylation modification sites based on Bruker ion trap mass spectrometry (amazon) data, the steps are as follows:

[0031] 1) Phosphopeptide database search:

[0032] The present invention is based on MASCOT and pFind database retrieval results, therefore, it is necessary to perform database retrieval first. The mass spectrometry data used in this example comes from the ion trap mass spectrometer amazon ETD of Bruker Company. The original data collected by the mass spectrometer is in the format of "*.yep". Use the company's software DataAnalysis4.0 software to perform peak conversion, export the results and save them as mgf format files, and then use the open source free software ProteoWizard to convert the data into standard mgf format file.

[0033] Open the local database search software MASCOT or pFind, import the mgf format data file, and set the relevant search parameters: trypsin digestion (trypsin), cysteine ​​alkylati...

Embodiment 2

[0052] Example 2: Identification of protein phosphorylation modification sites based on AB Sciex company TripleTOF4600 mass spectrometry data

[0053] In this embodiment, the data format collected by TripleTOF mass spectrometry is ".wiff", and the open source free software ProteoWizard can be directly used to convert the data into a standard mgf format file. Then search the MASCOT and pFind databases, relocate the phosphorylation modification sites, evaluate the reliability, and automatically export the spectra in batches. The specific implementation method is the same as that in Example 1.

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Abstract

The invention provides a method of identifying protein phosphorylation modification sites on the basis of tandem mass spectrometry. According to the method, application result data is searched by tandem mass spectrometry MGF-formatted (mascot generic file-formatted) data and mascot and pFind databases; programming is performed by a Perl language program; identified protein phosphorylation modification sites are re-located fast; and the re-located protein phosphorylation modification sites are calculated by a new scoring algorithm. The method is more creditable and also allows for fast automatic batch exporting of mass spectrograms related to the protein phosphorylation modification sites. The method has the advantages that operation is simple, locating information of the modification sites is highly creditable and the extracted mass spectrograms are high in resolution. The method is well applicable to the field of proteomics study.

Description

technical field [0001] The invention relates to the field of biological information, in particular to a method for identifying protein phosphorylation modification sites based on tandem mass spectrometry. Background technique [0002] Protein phosphorylation is the most common and important post-translational modification of proteins in the biological world. In cells, approximately one-third of proteins are thought to be phosphorylated. The reversible process of protein phosphorylation and dephosphorylation is a key link in the expression regulation of prokaryotic and eukaryotic cells, almost regulating cell proliferation, development, differentiation signal transduction, apoptosis, neural activity, muscle contraction and tumor Reversible protein phosphorylation is the most important signal transfer method known so far. Therefore, the analysis of protein phosphorylation and the identification of phosphorylation sites have become the concerns of many biochemists and proteom...

Claims

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Application Information

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IPC IPC(8): G06F19/28
Inventor 张珈杨明坤葛峰熊倩郑鹏李重阳
Owner INST OF AQUATIC LIFE ACAD SINICA
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