Simple and selective extraction method of C-and N-terminal ions in ESI-MS/MS analyses, named isotopic differentiation protocol (IDP), was developed. It takes advantage of the mass-difference between the isotopologues after methyl and deuterated methyl ester formations at the C-terminal carboxylic acid or acetamide and deuterated acetamide formations at the N-terminal amines. This method distinguishes the N-terminal and C-terminal ions in principle to facilitate the de novo peptide sequencing. An application with non-ribosomal depsipeptide plipastatin revealed that a pair of the peptide and the corresponding methyl ester at the C-terminus was also applicable to IDP method giving spectrum with enough quality. Facilitating software named "MSMS Search Tool" was also developed.