Method for analysis of compound-binding ability of protein

Abstract

A method for analyzing a binding ability of protein to a compound, involves fractionating first and second groups of proteins into plural fractions using a carrier having the compound immobilized thereon; combining fractions, analyzing the combined fractions with mass spectrometry; based on the mass spectrometry information, obtaining, regarding each fraction, an intensity ratio between peaks derived from a protein in each of the groups of fractions; and comparing degrees of the binding ability of the plural kinds of proteins to the compound.

1 . A method for analyzing a binding ability of protein to a compound, comprising:
 (a) fractionating a first group of proteins into plural fractions using a carrier having the compound immobilized thereon;   (b) adding a certain amount of a second group of proteins to each of the fractions obtained in step (a);   (c) analyzing the fractions obtained in step (b) with mass spectrometry; and   (d) based on the mass spectrometry information, obtaining, regarding each fraction, an intensity ratio between a peak derived from a protein in the fraction obtained in step (a) and a peak derived from a protein in the second group of proteins, and comparing degrees of the binding ability of the plural kinds of proteins to the compound.   
     
     
         2 . The method according to  claim 1 , wherein one of the first group of proteins and second group of proteins is isotope-labeled. 
     
     
         3 . The method according to  claim 1  further comprising labeling the fractions obtained in (a). 
     
     
         4 . The method according to  claim 3 , wherein the fractioning of (a) comprises changing the strength of an eluting solvent. 
     
     
         5 . The method according to  claims 4 , further comprising identifying each protein contained in each fraction based on the mass spectrometry information. 
     
     
         6 . The method according to  claim 5 , wherein the comparing the degrees of the binding ability of the plural kinds of proteins to the compound comprises determining that a protein concentrated in a fraction which is eluted later has a higher binding ability to the compound. 
     
     
         7 . The method according to  claim 1 , wherein (d) comprises determining that a protein concentrated in a fraction which is eluted later has a higher binding ability to the compound that an earlier eluted protein. 
     
     
         8 . The method according to  claim 1 , wherein the fractioning of (a) comprises changing the strength of an eluting solvent. 
     
     
         9 . The method according to  claims 1 , further comprising identifying each protein contained in each fraction based on the mass spectrometry information. 
     
     
         10 . The method according to  claim 3 , wherein the comparing the degrees of the binding ability of the plural kinds of proteins to the compound comprises determining that a protein concentrated in a fraction which is eluted later has a higher binding ability to the compound. 
     
     
         11 . The method according to  claim 2 , wherein the comparing the degrees of the binding ability of the plural kinds of proteins to the compound comprises determining that a protein concentrated in a fraction which is eluted later has a higher binding ability to the compound. 
     
     
         12 . The method according to  claim 1 , wherein the comparing the degrees of the binding ability of the plural kinds of proteins to the compound comprises determining that a protein concentrated in a fraction which is eluted later has a higher binding ability to the compound. 
     
     
         13 . A method for analyzing a binding ability of protein to a compound, comprising:
 (a1) fractionating a first group of proteins into plural fractions using a carrier having the compound immobilized thereon;   (a2) analyzing the fractions obtained in (a1) with mass spectrometry;   (a3) identifying each of the proteins in the fractions obtained in (a1) based on the mass spectrometry information obtained in (a2);   (a4) quantitating each of the proteins in the fractions obtained in (a1);   (b1) analyzing a second group of proteins with mass spectrometry;   (b2) identifying each protein in the second group of proteins based on the mass spectrometry information obtained in (b1);   (b3) quantitating each protein in the second group of proteins; and   (c) obtaining, regarding each fraction obtained in (a1), a ratio between the protein quantity obtained in (a4) and the protein quantity obtained in (b3), and comparing degrees of the binding ability of the plural kinds of proteins to the compound.   
     
     
         14 . The method according to  claim 8  wherein each of the quantitating comprises calculating an EMPAI of each of the proteins in the fractions; and the ratio is the ratio between the EMPAIs. 
     
     
         15 . The method according to  claim 9 , wherein the comparing the degrees of the binding ability of the plural kinds of proteins to the compound comprises determining that a protein concentrated in a fraction which is eluted later has a higher binding ability to the compound. 
     
     
         16 . A system for analyzing a binding ability of protein to a compound, comprising:
 (a) a fractionator for fractionating a first group of isotope-labeled proteins into plural fractions using a carrier having the compound immobilized thereon;   (b) a fractionator for fractionating a second group of proteins into one or plural fractions using a carrier having the compound immobilized thereon;   (c) a mixer for adding a certain amount of the one fraction obtained by fractionator (b), or a certain amount of a mixture of all the fractions or a mixture of plural contiguous fractions among the fractions obtained by fractionator (b), to each of the fractions obtained by fractionator (a);   (d) an analyzer for analyzing the fractions obtained by fractionator (c) with mass spectrometry; and   (e) a comparer for, based on the mass spectrometry information, obtaining, regarding each fraction, an intensity ratio between a peak derived from a protein in the fraction obtained by fractionator (a) and a peak derived from a protein in the fraction obtained by fractionator (b), and comparing degrees of the binding ability of the plural kinds of proteins to the compound.