High-resolution mass spectrometry confirms the presence of a hydroxyproline (Hyp) post-translational modification in the GGGGP linker of an Fc-fusion protein

Flexible and protease resistant (G4S)_n linkers are used extensively in protein engineering to connect various protein domains. Recently, several groups have observed xylose-based O-glycosylation at linker Ser residues that yield unwanted heterogeneity and may affect product quality. Because of this, an engineering effort was implemented to explore different linker sequence constructs. Here, we demonstrate the presence of an unexpected hydroxylation of a prolyl residue in the linker, made possible through the use of high-resolution mass spectrometry (HR-MS) and MS_n. The discovery started with the detection of a poorly resolved ～+17 Da mass addition at the reduced protein chain level of an Fc-fusion construct by liquid chromatography-MS. Upon further investigation at the peptide level using HR-MS, the mass increase was determined to be +15.99 Da and was localized to the linker peptide SLSLSPGGGGGPAR 210–223]. This peptide corresponds to the C-terminus of Fc 210–216], the G4P linker 217–221], and first 2 amino acids of a growth factor 222–223]. The linker peptide was first subjected to MS² with collision-induced dissociation (CID) activation. The fragmentation profile localized the modification to the GGGPA 218–222] portion of the peptide. Accurate mass measurement indicated that the modification is an addition of an oxygen and cannot be CH₄, thus eliminating several possibilities such as Pro→Leu. However, other possibilities cannot be ruled out. Higher-energy collision-induced dissociation (HCD)-MS² and MS³ using CID/CID were both unable to differentiate between Ala222→ Ser222 or Pro221→ Hyp221. Finally, MS³ using high-resolution CID/HCD confirmed the mass increase to be a Pro221→Hyp221 post-translational modification.