A method for analyzing a structural affinity relationship between plural kinds of proteins and a compound, comprising the steps of (a) using a compound-immobilized carrier to purify plural kinds of proteins bound to the compound on the carrier, from a group of isotope-labeled proteins; (b) using a compound-immobilized carrier to purify plural kinds of proteins bound to the compound on the carrier, from a group of proteins brought into contact with a compound beforehand; (c) mixing the proteins obtained in step (a) and step (b); (d) analyzing the mixture obtained in step (c) with mass spectrometry; (e) identifying each of plural kinds of proteins based on information obtained by the mass spectrometry; and (f) obtaining an intensity ratio between a labeled peak and a non-labeled peak of each protein, thereby quantitating an affinity ratio of the compound to each protein.