A method of analysis for a formylglycine residue and a cysteine residue in the amino acid residues that makes up an analyte protein comprising, (a) a step of converting the protein respectively into (i) a halogen-substituted carboxylic acid-labeled protein by labeling the protein with a halogen-substituted carboxylic acid, (ii) a halogen-substituted carboxylic acid amide-labeled protein by labeling the protein with a halogen-substituted carboxylic acid amide, and (iii) a halogen-substituted carboxylic acid-hydrazine-labeled protein or a halogen-substituted carboxylic acid-oximation-labeled protein by labeling the protein with a halogen-substituted carboxylic acid and then with hydrazine or by labeling with halogen-substituted carboxylic acid and then by oximation, (b) a step of digesting each of the labeled proteins to provide a corresponding mixture of peptide fragments, (c) a step of subjecting each mixture of peptide fragments to reverse phase chromatography to separate the peptide fragments from each other while monitoring the separated fragments with absorptiometer, producing a chromatogram of the mixture of peptide fragments, (d) a step of comparing the produced chromatograms with each other to identify, on the chromatograms, the peak corresponding to a peptide fragment which contained a cysteine residue when in the analyte protein and the peak corresponding to a peptide fragment which contained a formylglycine residue when in the analyte protein. (a) a step of converting the protein respectively into (i) a halogen-substituted carboxylic acid-labeled protein by labeling the protein with a halogen-substituted carboxylic acid, (ii) a halogen-substituted carboxylic acid amide-labeled protein by labeling the protein with a halogen-substituted carboxylic acid amide, and (iii) a halogen-substituted carboxylic acid-hydrazine-labeled protein or a halogen-substituted carboxylic acid-oximation-labeled protein by labeling the protein with a halogen-substituted carboxylic acid and then with hydrazine or by labeling with halogen-substituted carboxylic acid and then by oximation, (i) a halogen-substituted carboxylic acid-labeled protein by labeling the protein with a halogen-substituted carboxylic acid, (ii) a halogen-substituted carboxylic acid amide-labeled protein by labeling the protein with a halogen-substituted carboxylic acid amide, and (iii) a halogen-substituted carboxylic acid-hydrazine-labeled protein or a halogen-substituted carboxylic acid-oximation-labeled protein by labeling the protein with a halogen-substituted carboxylic acid and then with hydrazine or by labeling with halogen-substituted carboxylic acid and then by oximation, (b) a step of digesting each of the labeled proteins to provide a corresponding mixture of peptide fragments, (c) a step of subjecting each mixture of peptide fragments to reverse phase chromatography to separate the peptide fragments from each other while monitoring the separated fragments with absorptiometer, producing a chromatogram of the mixture of peptide fragments, (d) a step of comparing the produced chromatograms with each other to identify, on the chromatograms, the peak corresponding to a peptide fragment which contained a cysteine residue when in the analyte protein and the peak corresponding to a peptide fragment which contained a formylglycine residue when in the analyte protein.