The present invention provides a method for analyzing a binding ability of protein to a compound, comprising the steps of (a) fractionating a first group of isotope-labeled proteins into plural fractions using a carrier having the compound immobilized thereon; (b) fractionating a second group of proteins into one or plural fractions using a carrier having the compound immobilized thereon; (c) adding a certain amount of the one fraction obtained in step (b), or a certain amount of a mixture of all the fractions or a mixture of plural contiguous fractions among the fractions obtained in step (b), to each of the fractions obtained in step (a); (d) analyzing the fractions obtained in step (c) with mass spectrometry; and (e) 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 fraction obtained in step (b), and comparing degrees of the binding ability of the plural kinds of proteins to the compound.