Isobaric Tandem Mass Tag Multiplexed Post-Translational Modification Quantitation of Biopharmaceuticals by Targeted High-Resolution Mass Spectrometry

Peptide mapping coupled with liquid chromatography–mass spectrometry (LC–MS) has become an essential analytical technique to quantify the quality attributes (e.g., post-translational modifications [PTMs]) of monoclonal antibodies (mAbs) during drug development. However, the traditional label-free approach for relative quantitation of PTMs requires a great amount of instrument time for LC–MS data acquisition of individual digested samples, which limits the efficiency of peptide mapping when there is an increasing demand for protein characterization. Here, we developed a tandem mass tag (TMT)-based approach in combination with targeted mass spectrometry for multiplexed site-specific PTM quantitation of monoclonal antibodies to overcome this limitation. This approach enables the simultaneous quantitation of quality attributes (e.g., PTMs) for multiple samples in a single LC–MS run. By adjusting higher-energy collision dissociation (HCD) normalized collisional energies (NCEs) from 35 to 90, different types of PTMs were quantified with percentages comparable to those obtained using the conventional approach. The TMT overlabeling on the off-target amino acid residues serine, threonine, and tyrosine was observed to pose a challenge for this targeted MS/MS-based PTM quantitation. However, we inhibited this off-target overlabeling by adding a small-molecule additive during the TMT labeling as a decoy reagent to deplete the excess amount of TMT reagent. The PTM quantitative performance of this approach demonstrated high sensitivity and reproducibility of PTM quantitation with levels as low as 1.0%. Finally, this approach has been utilized to quantify the PTMs for forced degradation samples, comparability samples, and trisulfide standards of monoclonal antibodies.