To provide a method capable of analyzing easily structure of a protein by mass spectrometric analysis, in mass spectrometry using the protein with a modified group coupled via a thioether group, that is one kind of a protein with lipid such as a protein containing an amino acid moiety with the lipid coupled via the thioether group, as a main target.

In this mass spectrometry for the protein containing sulfur atom, the protein (a) containing the amino acid moiety with an alkyl group containing a hydroxyl group coupled via the thioether group is prepared, the protein (a) is oxidized by making an oxidant act thereon to obtain a protein (b) with oxidized sulfur atom of the thioether group, and the oxidized protein (b) is measured using a mass spectrograph.

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