A hydrolyzed N‐propionylthiosuccinimide linker is cleaved by metastable fragmentation, increasing reliability of conjugation site identification in conjugate vaccines

Abstract RATIONALE Conjugation sites are a quality attribute of conjugate vaccines. Proteolysis of bioconjugates synthesized by maleimide–thiol chemistry generates type 2 peptides with a hydrolyzed thiosuccinimide linker containing information on the conjugation sites. A mass spectrometry (MS)‐cleavable linker could make the identification of conjugation sites by MS more reliable. METHODS Four synthetic type 2 peptides with a hydrolyzed thiosuccinimide linker were analyzed by matrix‐assisted laser desorption ionization (MALDI) MS/MS with and without collision gas. These peptides were also partially labeled with 18 O in the linker to confirm the proposed fragmentation mechanism. A conjugate vaccine with the hydrolyzed thiosuccinimide linker was reduced and S ‐alkylated, digested with trypsin and analyzed by liquid chromatography–MS/MS using collision‐induced dissociation (CID) and higher‐energy collisional dissociation (HCD) fragmentation methods at a normalized collision energy of 30. RESULTS A metastable fragmentation preferentially cleaves the newly formed pseudopeptide bond within the hydrolyzed thiosuccinimide linker of type 2 peptides to yield P + 71 and C + 98 ions. These ions make the assignment of conjugation sites more reliable. Partial 18 O‐labeling and MS/MS analysis confirmed the proposed structures. CID produces these ions as the two most intense signals more favorably than HCD. The latter also yields these ions, guarantees better sequence coverage and promotes other fragmentations in the linker. CONCLUSIONS Hydrolyzed thiosuccinimide linker is cleavable in MALDI and electrospray ionization MS/MS analysis by a gas‐phase metastable fragmentation. The resulting fragment ions (P + 71 and C + 98) make the identification of conjugation sites more reliable. These results could be extended to self‐hydrolyzing maleimides, which efficiently stabilize the thiosuccinimide linker upon hydrolysis, in antibody–drug conjugates.