Looking for breakthrough ideas for innovation challenges? Try Patsnap Eureka!

Method for identification of protein by utilizing high-energy collision induced ionization dissociation technology

A protein and high-energy technology, applied in the field of bioinformatics, can solve problems such as limited modification types, no pre-screening method for HCD data modification types, optimization of the construction method of the library and the search engine of the library, etc., to improve the identification success rate, The effect of improving identification sensitivity and improving peptide identification sensitivity

Active Publication Date: 2014-04-02
INST OF RADIATION MEDICINE ACAD OF MILITARY MEDICAL SCI OF THE PLA
View PDF3 Cites 14 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0010] (1) Conventional search engines such as MASCOT, SEQUEST, and X!Tandem have not designed corresponding theoretical maps and matching scoring methods for HCD, and the processing of HCD still uses the same theoretical spectrum and scoring methods as CID;
[0011] (2) Quality control methods for peptide identification do not make full use of HCD data characteristics
[0012] (3) The existing de novo sequencing algorithm for HCD maps considers limited modification types, and there is no pre-screening method for modification types for HCD data.
[0013] (4) In terms of spectral library search, there are no spectral library construction methods and spectral library search engines optimized for HCD data (Lam 2011)

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 more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Method for identification of protein by utilizing high-energy collision induced ionization dissociation technology
  • Method for identification of protein by utilizing high-energy collision induced ionization dissociation technology

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0036] Example 1. Using HCD tandem MS / MS data to analyze and identify peptide sequences

[0037] 1. Enzymatic hydrolysis to obtain peptides

[0038] Saccharomyces cerevisiae strain ATCC 201388 (BY4741, MATa his3delta1 leu2delta0 met15delta0ura3delta) was purchased from American Type Culture Collection.

[0039] Strain culture: use YPD medium to cultivate yeast ATCC 201388, culture on a constant temperature shaker at 30°C until OD600 is 1.5, collect the bacteria by centrifugation at 5000rpm for 5 minutes, pour out the supernatant, and rinse the precipitate with 0.1% sodium azide phosphate buffer After centrifuging to remove the supernatant, the cells were collected and stored in a -80°C refrigerator.

[0040] Cell lysis: add urea lysate (8M urea, 50mM ammonium bicarbonate, 50mM iodoacetamide) to the yeast cell precipitation, then add glass beads equal to the cell volume, and place it on a vortex mixer at the maximum speed Vortex to lyse for 5 minutes, centrifuge at 13000 rpm ...

Embodiment 2

[0068] Example 2. Optimization of Peptide Sequence Analysis and Identification Using HCD Tandem MS / MS Spectrogram Data

[0069] The HCD secondary mass spectrograms of 16,479 peptides obtained in 2 of Example 1 were processed according to the basic method of Step 3 and Step 4 of Example 1 as follows:

[0070] C1 is the first isotope peak added, and "only y" is the isotope peak with only y ions added. "only y"+C1 is the best condition, that is, only the first isotope peak of y ion is added. C0 means no isotopic peaks added.

[0071] A, "b&y"+C0 treatment group (for the control group in Example 1)

[0072] B. "b&y"+C1 treatment group

[0073] B.1) Format conversion: the method is the same as step 3 of embodiment 1;

[0074] B.2) Search, generate theoretical spectrum and match scoring: basically the same as Step 4 of Example 1, the difference is that in the theoretical spectrum, except for the mass-to-charge ratio of the b and y ion monoisotope peaks of candidate peptides and ...

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

No PUM Login to View More

Abstract

The invention discloses a method for identification of a protein by utilizing high collision induced dissociation. The invention provides the method for identification of the unknown target protein by utilizing high collision induced dissociation. The method comprises the following main steps: adopting a search engine for candidate peptide fragment searching of obtained second-level HCD mass spectrograms, and generating a theoretical spectrum; and then matching an experimental spectrum with the theoretical spectrum, and outputting identification results. The generation of the theoretical spectrum comprises simultaneously generating theoretical b ion monoisotopic peak mass-to-charge ratios, generating theoretical y ion monoisotopic peak mass-to-charge ratios and increasing first isotopic peak ion mass-to-charge ratios of y ions. The method is simple and effective, and can significantly improve the peptide fragment identification sensitivity without changing a database search engine data structure and a matched grading algorithm.

Description

technical field [0001] The invention relates to the field of bioinformatics, in particular to a method for identifying proteins using high-energy collision-induced ionization fragmentation technology. Background technique [0002] With the development of mass spectrometry, high-energy collision fragmentation (HCD, high-energy collision induced dissociation) is widely used in the qualitative and quantitative identification of proteome expression profiles and modification profiles (Olsen, Macek et al.2007; Nagaraj, D'Souza et al. 2010; Savitski, Mathieson et al. 2010; de Graaf, Altelaar et al. 2011; Frese, Altelaar et al. 2011). The output sensitivity of the HCD secondary spectrum of the new generation of high-precision mass spectrometer LTQ-OrbiTrap Velos is close to or equivalent to that of CID (collision induced dissociation), both of which are higher than the electron transfer fragmentation (ETD, electron transfer dissociation) spectrum, but the quality of the HCD spectrum...

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
no application Login to View More
IPC IPC(8): G01N30/86
Inventor 徐平李宁
Owner INST OF RADIATION MEDICINE ACAD OF MILITARY MEDICAL SCI OF THE PLA
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Patsnap Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Patsnap Eureka Blog
Learn More
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic, Popular Technical Reports.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com