Mass Spectrometry and 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 structural characterization and proteomic analytical services.

Mass Spectrometry Services

Nanoflow LC – MS/MS (GMP)

  • Columns: Reversed Phase (RP) C4-C18, HILIC
  • LC-Detector: UV
  • Source: ESI (Electron Spray Ionization)

Why use LC-MS GMP?

LC‑MS is already one of the most powerful analytical tools in biopharma. Conducting these analyses under GMP elevates their regulatory value and makes the results acceptable for clinical and commercial decision‑making.

The advantages of GMP LC-MS:

  • LC‑MS enables GMP-compliant QC release, stability testing, and impurity profiling
  • Fully qualified instruments (IQ/OQ/PQ) and validated methods
  • Data integrity & 21 CFR Part 11 compliance
  • Supports analysis of CQAs (identity, purity, PTMs, glycosylation, impurities) in biologics
  • Regulatory alignment (FDA, EMA, ICH Q14/Q6B/Q8)
  • Superior sensitivity, specificity & ability to replace less sensitive methods
  • GMP LC‑MS reduces false positives and improves trace-level detection
  • Required for regulatory submissions and routine operations

Host cell proteins (HCP)

  • Quantitative proteomics using tandem mass tags (TMT), targeted absolute quantification (AQUA), spike-in peptides for semi-quantitation, and label-free quantitation
  • Proteome via shotgun LC-MS approach
  • HCP antibody coverage via affinity chromatography and LC-MS

Proteins including mAB and glycoproteins

  • Quantitative proteomics using tandem mass tags (TMT), absolute quantification (AQUA), and label-free quantitation
  • Amino acid sequence verification via peptide mapping, LC-MS
  • Intact and Subunit molecular mass analysis by LC-MS
  • De novo amino acid sequencing via peptide mapping, LC-MS
  • Disulfide bond mapping via peptide mapping, LC-MS
  • Characterization of post-translational modifications via peptide mapping, LC-MS, including deamidation, oxidation, pyroglutamate formation and glycosylation sites

Adeno-associated viruses (AAV)

  • Quantitative proteomics using tandem mass tags (TMT), absolute quantification (AQUA), and label-free quantitation
  • Amino acid verification via peptide mapping, LC-MS
  • Molecular weight via intact mass, LC-MS
  • Proteomic post-translational modifications (PTM) identification and quantification including phosphorylation pathway mapping/profiling, acetylation, methylation
  • Intact Capsid Protein MW and Ratio Analysis (VP1, VP2, VP3) (GMP)

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 the Orbitrap Fusion Lumos 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 Lumos) coupled with liquid chromatography. Proteins are identified from several or many unique peptides corresponding to each protein via protein database searching.

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