Mass Spectrometry & Structural Characterization

With over 20 years of experience in mass spectrometry services, we have a proven track record supporting diverse protein characterization programs including large molecule comparability studies. Our experience managing complex mass spectrometry projects combined with our state-of-the-art instrumentation and infrastructure allows us to deliver high quality GMP structural characterization and proteomic analytical services.

Webinar: Mass Spectrometry-Based Characterization


See how utilizing a modern mass spectrometer can determine amino acid sequences and sequential fragmentation.

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Our mass spectrometry services include:

  • Peptide mapping of antibodies and complex glycoproteins
  • Intact and subunit molecular weight determination
  • Glycan structural characterization, including de novo analysis
  • Glycosylation site mapping and site occupancy determination host cell protein (HCP) analysis
  • Quantitative proteomics using tandem mass tags (TMT), absolute quantification (AQUA), and label-free quantitation 
  • Cellular/tissue proteomic post-translational modifications (PTM) identification and quantification including phosphorylation pathway mapping/profiling, acetylation, methylation, and ubiquitination
  • Disulfide bond mapping and isoform characterization 
  • PEGylation site mapping
  • Antibody-drug conjugate (ADC) stoichiometry and conjugation-site characterization
  • Glycosaminoglycans (GAGS), heparin, and heparan sulfate 
  • Lipid and phospholipid profiling
  • Glatiramer acetate comparability
  • De novo amino acid sequencing, including Ile/Leu determinations
  • Peptide mapping using ICH validation methods for GMP lot release
  • Biosimilar comparability and characterization programs
  • Degradation, forced degradation, and stability studies 
  • Reference standard characterization

With extensive experience in mass spectrometry services and managing complex analytical projects, you can trust us as a partner in your drug development journey.  

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Frequently Asked Questions (FAQs) for Mass Spectrometry Services

  • What is molecular weight determination?

    Molecular weight, or molecular mass, is the total mass of a molecule based on the atomic masses of its individual atoms. By providing mass determination with low measurement errors (parts per million, ppm), mass spectrometry enables precise determination of molecular composition.

  • What is Orbitrap Fusion and how is it used for structural characterization?

    The Thermo Scientific™ Orbitrap Fusion™ mass spectrometer is a unique hybrid instrument combining quadrupole, Orbitrap, and linear ion trap mass analysis features including: 

    • Ultrafast scan rates
    • High resolution mass measurement 
    • MS/MS ion selection

    With three fragmentation modes (CID, HCD, ETD) including multi-stage fragmentation, the system provides a highly flexible platform for biological drug product characterization.

  • How is peptide mapping performed using mass spectrometry services?

    Peptide mapping is used to confirm protein primary structure by determining its amino acid sequence and employing endoproteases (enzymes) to generate peptides, followed by analysis by HPLC coupled with mass spectrometry. 
    Importantly, peptide mapping also enables localization of post-translational modifications (PTMs) including: 

    • N- and O-linked glycosylation 
    • N-terminal pyroglutamic acid 
    • Acetylation/formylation 
    • C-terminal lysine clipping
    • Protein stability-indicating modifications including deamidation and oxidation events
    • Molecular fingerprints
  • How are proteomics services performed using mass spectrometry services?

    Proteomics, or protein identification, employs tandem mass spectrometry (MS/MS) of proteolytically generated peptides from a biological sample using a high-resolution mass spectrometer ( e.g., the Orbitrap Fusion) coupled with liquid chromatography. Proteins are identified from several or many unique peptides corresponding to each protein via protein database searching.