A universal buffer system for native LC-MS analysis of antibody-based therapeutics

Liquid chromatography coupled to mass spectrometry (LC-MS) is a powerful analytical technique for analyzing biological macromolecules. A long-standing challenge has been applying LC-MS at physiological pH under native conditions using volatile buffers. The predominant "buffer" used, ammonium acetate (AmAc, pKa 4.75 for acetic acid and 9.25 for ammonium), does not offer sufficient buffering capacity in the physiological pH range of 7.0-7.4. To address this, we evaluated a set of fluorinated ethylamines, 2-fluoroethylamine (MFEA, pKa 8.9), 2,2-difluoroethylamine (DFEA, pKa 7.2), and 2,2,2-trifluoroethylamine (TFEA, pKa 5.5), that together provide buffering across the 4.5-9.8 pH range. We show that protein separations on strong cation- and anion-exchange resins in these volatile mobile phases perform comparably to traditional non-volatile buffers, with similar elution profiles and analyte elution ranking, albeit with slightly broader peaks. Using fully volatile gradients of pH or ionic strength, we chromatographically resolved charge variants of protein analytes such as mAbs and bovine serum albumin. For many of the eluting LC peaks, we obtained high-resolution mass spectra capable of resolving glycoforms of antibodies. Hydrophobic interaction chromatography (HIC) in volatile mobile phases preserved native separation order and further resolved drug-to-antibody ratio (DAR) species of the antibody-drug conjugate brentuximab-vedotin. For each chromatography modality we further compare innovator and biosimilar antibodies, demonstrating the reproducibility of results in the proposed volatile compounds. Together, our results establish fluorinated ethylamines, in combination with ammonium acetate, as a universal volatile buffer system for native LC-MS, broadly applicable across major chromatographic modalities while maintaining compatibility with mass spectrometry.