Tsukidate, T.; Wang, Z.; Hsieh, A.; Rose, P.; Li, X.

Monoclonal antibodies (mAbs) are crucial biotherapeutics with increasing global demand, but their production can be impacted by the reduction of disulfide bonds. This study presents a chemical proteomics workflow aimed at elucidating the mechanisms underlying disulfide bond reduction in mAbs produced from Chinese hamster ovary (CHO) cells. We employed iodoacetamide-desthiobiotin (IA-DTB) and the parallel accumulation and serial fragmentation combined with data-independent acquisition (diaPASEF) methodology for cysteine reactivity profiling and successfully quantified approximately 4,500 cysteine-containing peptides from harvested cell culture fluids (HCCF). Our findings reveal that various protein disulfide oxidoreductases were active in reducing HCCF, offering critical insights into the redox environment affecting mAb stability. Notably, we quantified specific cysteine residues in enzymes such as glutaredoxin and thioredoxin domain-containing protein 12, suggesting potential links between their activity to disulfide bond dynamics. This workflow not only complements conventional abundance proteomics but also enhances the understanding of functional enzyme states in bioprocessing. Ultimately, our approach provides a promising strategy for enzymes contributing to disulfide bond reduction, paving the way for improved manufacturing processes of mAbs.