Patent ID: 8071392

Claim:
A method for determining the quantitative ratio of a target protein contained in two or more kinds of protein-containing samples using a mass spectrometer, which method comprises: (i) providing two or more kinds of protein-containing samples to be analyzed; (ii) preparing an internal standard sample by preparing starting samples with the same total protein content from all the corresponding protein-containing samples to be analyzed, and mixing equal amounts of the starting samples to obtain the internal standard sample; (iii) labeling the target protein in each of the protein-containing samples to be analyzed and the internal standard sample with a combination of two or more kinds of stable isotopes of a compound represented by the formula (I): wherein R 1 , R 2 and R 3 are the same or different and each is hydrogen, halogen or alkyl, or a salt thereof having a different mass number due to isotope, thereby producing a difference in the mass of the target protein contained in each of the protein-containing samples and the internal standard sample; (iv) mixing the respective protein-containing samples and the internal standard sample; (v) (a) separating the target protein in the mixture obtained in step (iv) from other proteins and cleaving the target protein with a restriction enzyme at a particular amino acid site to give a sample containing isotope-labeled peptides derived from the target protein, or (b) cleaving the target protein in the mixture obtained in step (iv) with a restriction enzyme at a particular amino acid site to give a sample containing isotope-labeled peptides derived from the target protein; and (vi) measuring an MS spectrum of the isotope-labeled peptides derived from the target protein determining an MS spectral intensity of each of the same kind of peptide derived from the target protein having a mass difference due to isotope labeling, determining the ratios of the MS spectral intensity derived from the protein-containing samples to the MS spectral intensity derived from the internal standard sample, determining the quantitative ratio based on the intensity ratios, and correcting the quantitative ratio by removing the overlap with the isotope peak of the peptide due to naturally occurring isotope.