When a conjugate vaccine is digested with specific proteases a complex mixture of peptides is generated . The type 2 peptides are those that contain useful information on the conjugation sites . They are composed by two crosslinked peptides, one derived from the carrier protein and the other from the antigen covalently linked by the thiosuccinimide linker or its stabilized forms (Figure ). To identify the conjugation sites of conjugate vaccines by the LC-MS/MS analysis we have used the same software that assign MS/MS spectra to type 2 peptides .