Mass Spectrometry for Protein Characterization

Mass spectrometry is among the most powerful analytical techniques available for protein characterization. KBI’s state-of-the-art mass spectrometry core facility delivers unparalleled structural characterization services to our clients.

Our expert team brings decades of experience in protein and peptide characterization to provide the right data with the right insight at all stages of development.

Whether you are seeking sequence verification and developability data to support proof-of-concept, initial structural characterization to support IND filing, or comprehensive impurity characterization to support BLA licensure, KBI will exceed your expectations.


Our experience in mass spectrometry characterization includes:

  • Monoclonal antibodies (full length mAbs, domain antibodies, antibody conjugates, fragments)
  • Fusion proteins
  • Multi-specific antibodies & proteins
  • Protein vaccines
  • Biosimilars, Biobetters, Biosuperiors
  • Other recombinant protein drugs
  • Proteomic work flows
    • Host Cell Proteins
  • Peptide drugs

KBI’s Mass Spectrometry Core Facility Capabilities

    • Waters Acquity® UPLC – Sciex TripleTOF® 6600

    • Waters Acquity® UPLC – Xevo® G2 Q-Tof

    • Waters Acquity® UPLC – Xevo® G2-S Q-Tof

    • Waters Acquity® UPLC – Xevo® G2-XS Q-Tof

    • Synapt ® G2-Si High Definition Mass Spectrometer

    • UPLC-UV/MS, UPLC-UV/MS/MS, UPLC-UV/MSE, UPLC-FLR/MSE, UPLC‑UV/SWATH

    • BiopharmaLynx™was a problem saving your data. pleaseJu, Progenesis QI for proteomics, BioLynx®, ProteinPilot™, BioPharmaView™, MultiQuant™, MarkerView™, PeakView™

    • Intact mass analysis by RP-UPLC-UV/MS, determination of glycosylation patterns

    • Separation and characterization of deglycosylated and/or reduced mAbs and fusion proteins by RP-UPLC-UV/MS

    • Intact mass analysis by RP-UPLC-UV/MS of reduced and non-reduced subunits following IdeS treatment for hinge region cleavage

    • Heterodimer purity analysis by RP-UPLC-UV/MS

    • Peptide mapping by RP-UPLC-UV/MSE for sequence confirmation

    • Modification / degradation analysis including glycosylation; N-terminal pyroglutamic acid, pyroglutamine; C-terminal lysine truncation; deamidation; oxidation; etc.

    • N-terminal & C-terminal processing and sequence heterogeneity assessment and quantitation by RP-UPLC-UV/MSE

    • Sequence variant identification by RP-UPLC-UV/MSE

    • Targeted peptide verification by RP-UPLC-UV/MS/MS

    • Quantitative monitoring of peptides or post-translationally modified peptides under cGMP conditions

    • Disulfide mapping by RP-UPLC-UV/MSE

    • RapiFluor labeled glycan identification and quantification of released N-glycans by HILIC UPLC-FLR/MSE

    • Glycan site occupancy from deglycosylated & reduced peptide map by RP-UPLC-UV/MSE

    • Site specific glycan profiling of fully glycosylated & reduced peptide map by HILIC-UPLC-UV/MSE

    • Host cell protein analysis

      • Spectral library generation
      • ELISA support
      • Monitoring process clearance
      • Identification and relative quantitation
      • Targeted screening and quantitation
    • PEGylation site and occupancy analysis

    • Product and process related impurity analysis

    • Cell line profiling

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