A method for predicting the quantitative efficiency of peptides in proteomics
A proteomics and peptide technology, applied in the field of peptide quantitative efficiency prediction, which can solve the problems of complexity and many factors of peptide quantification.
Active Publication Date: 2020-06-05
ACAD OF MATHEMATICS & SYSTEMS SCIENCE - CHINESE ACAD OF SCI +2
View PDF3 Cites 0 Cited by
- Summary
- Abstract
- Description
- Claims
- Application Information
AI Technical Summary
Problems solved by technology
However, there are many and complex factors that affect the quantification of peptides, and the quantification of each peptide alone cannot eliminate the error well
Method used
the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View moreImage
Smart Image Click on the blue labels to locate them in the text.
Smart ImageViewing Examples
Examples
Experimental program
Comparison scheme
Effect test
Embodiment Construction
[0077] The present invention will be further described below in conjunction with the accompanying drawings and specific embodiments.
[0078] Suppose you have a protein sample. First, the protein mixture sample is enzymatically hydrolyzed by existing biochemical techniques to form a peptide mixture solution, and then experimental tandem mass spectrometry data are generated by liquid chromatography-mass spectrometry. The tandem mass spectrometry data includes three-dimensional information of chromatographic retention time, particle mass-to-charge ratio, and mass spectrometry response signal intensity. Next, it is necessary to extract the mass spectrum signal intensity of the peptide from the spectral data through the peptide signal intensity extraction tool, such as MaxQuant (reference: Cox, J. and Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol, 2008, 26, pp 1367-...
the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More PUM
Login to View More Abstract
The invention discloses a peptide fragment quantification efficiency prediction method of peptide fragments in proteomics. The method comprises the steps of: 1) screening out highly-trusted proteins,and using identified peptide fragments of the highly-trusted proteins as highly-trusted fragments; 2) calculating physicochemical properties and peptide fragment quantification efficiency of the highly-trusted peptide fragments, wherein the peptide fragment quantification efficiency is degrees of reaction which is of mass-spectrum signal intensity of the peptide fragments and to real quantity of the peptide fragments; 3) constructing a training set of a model, which predicts peptide fragment quantification efficiency, on the basis of the physicochemical properties and the peptide fragment quantification efficiency of the highly-trusted peptide fragments, and then using the training set to obtain the peptide fragment quantification efficiency prediction model by training; and 4) using the peptide fragment quantification efficiency prediction model to predict peptide fragment quantification efficiency of each identified peptide fragment of an identified protein. According to the method of the invention, the highly-trusted peptide fragments are used to construct the training set, online training of the peptide fragment quantification efficiency is carried out, and errors caused by experiment operations, experiment instruments and the like are eliminated.
Description
technical field [0001] The invention relates to the research on peptides and protein quantification methods in proteomics based on mass spectrometry, in particular to a method for predicting peptide quantification efficiency. Background technique [0002] After identifying proteomics, quantitative proteomics has become the next research hotspot in the field of life sciences. Its research mainly includes labeled and unlabeled quantification of proteins based on mass spectrometry data. Although label-free quantification is not as accurate as labeled quantification, label-free quantification is still the preferred method in large-scale protein quantification due to its advantages of simple operation and low cost. [0003] The ideal experimental method for protein quantification is to add an internal standard for each protein, however, this practice means high cost for the analysis of complex samples. At present, the most commonly used method is the method of linear fitting ca...
Claims
the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More Application Information
Patent Timeline
Login to View More Patent Type & Authority Patents(China)
IPC IPC(8): G16B30/00G16B40/00
CPCG16B40/00
Inventor 付岩常乘高志强朱云平
Owner ACAD OF MATHEMATICS & SYSTEMS SCIENCE - CHINESE ACAD OF SCI