Aim of the project
This master project has two major aims. One aim is to advance high throughput monoclonal antibody characterization using MALDI-MS. The other aim is to improve host cell protein (HCP) impurity analyses by evaluating different approaches based on antibody-binding magnetic beads, and molecular weight cutoff devices in combination with LC-MS.
Background
Biologics are medicines that contain substances produced using living cells or organisms. Over the past 25 years, biologics such as monoclonal antibodies (mAbs) have revolutionized the pharmaceutical industry and patient care. More than 200 antibodies have been approved by the FDA and EMA, generating annual sales of over €150 billion. Notably, four of the ten top-selling drugs in 2025 were monoclonal antibodies (mAbs). The comprehensive characterization of biologics and their associated impurities is a major priority for the biopharmaceutical industry. In particular, the thorough characterization of mAbs is essential for both manufacturing and regulatory approval. Product efficacy and safety are governed by specific molecular features known as critical quality attributes (CQAs).
Liquid chromatography-mass spectrometry (LC-MS) and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) are cornerstone techniques in modern protein analysis. LC-MS plays a major role in the analytical characterization of mAbs. In general, mAbs can be characterized as intact molecules, subunits, as well as peptides after enzymatic digestion using mass spectrometry.
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Project
i. Monoclonal antibody characterization using MALDI-MS
LC-MS is currently the standard analytical platform for monoclonal antibody characterization by mass spectrometry. In contrast, MALDI-MS offers simpler operation and enables high-throughput analysis by omitting peptide separation using LC. This project therefore aims to assess whether MALDI-MS can be used as an alternative to LC-MS for mAb characterization. Both intact protein mass determination and peptide mapping using different endoproteases will be investigated. Several mAbs (bevacizumab, cetuximab, NISTmAb, trastuzumab, and trastuzumab-based ADCs) will be evaluated.
- Improved host cell protein (HCP) impurity analysis using LC-MS
HCPs derive from the biotechnological manufacturing process of the therapeutic proteins. Chinese hamster ovarian (CHO) cells are commonly used to produce therapeutic proteins. HCPs can contaminate the product and can reduce the effectiveness of the drug or cause side effects in patients. LC-MS is able to identify and quantify HCPs without prior knowledge of the identity of the proteins. Antibodies are produced in high amounts and impurities are minor after purification by protein A and further chromatographic purification steps. Thus, the detection and characterization of HCPs by LC-MS peptide mapping is challenging because they are typically present at very low levels (<100 ppm).
Different sample-preparation strategies, such as magnetic bead-based methods and molecular weight cutoff (MWCO) filters, will be evaluated to increase the number of host cell protein (HCP) identifications in mAb preparations. HCP analysis will be performed by LC-MS, which offers a higher dynamic range (the ratio between the maximum and minimum signal that can be accurately measured) than MALDI-MS.
Main methods and materials
As a Master student, you will develop a strong background in protein analytical techniques which include laboratory techniques for sample preparation, familiarization with sophisticated instrumentation (MALDI-MS and LC-MS), and protein data analysis.
The LC-MS instrument (NanoElute LC coupled to TimsTOF Pro mass spectrometer) is established and maintained by an engineer in the proteomics laboratory. A novel MALDI-MS instrument (NeofleX) will be installed in autumn 2026 at the Life Science building.
The project will start with using commercially available mAbs. Bevacizumab, cetuximab, and trastuzumab are antibodies which reveal high sequence coverages using trypsin. The NISTmAb antibody is used as a reference standard in the biopharmaceutical industry.
Research environment and supervision:
The project will be performed at the Proteomics Core Facility.
https://www.mn.uio.no/ibv/english/research/sections/bmb/research-groups/proteomics-thiede/about/
If you find this project interesting or have any questions, please contact bernd.thiede@ibv.uio.no