PhD position Finding Molecular Glyco(proteo)mic Signatures by Mass Spectrometry

University of Groningen

The University of Groningen provides a fully funded PhD scholarship in the field of mass spectrometry in the research group of Dr Guinevere Lageveen-Kammeijer. The position is based at the Analytical Biochemistry group, embedded in the Groningen Research Institute of Pharmacy (GRIP) and is a dynamic multidisciplinary group of researchers stemming from the fields of (computational) MS, proteomics and metabolomics.

This PhD project aims to develop the urgently needed analytical tools to decipher and characterize the malignant sugarcode of tumor cells using minimal sample amounts (e.g. single cell analysis). For this purpose, the candidate will develop new sample preparation strategies as well as optimize high-end analytical platforms (nano-liquid chromatography and capillary electrophoresis hyphenated with state-of-the-art mass spectrometers). It is expected that numerous glycomic and glycoproteomic profiles will be generated from various biological samples (e.g. tissues, blood and urine), which will require the development of new data analysis strategies. The obtained information will be used to find glycomic alterations in the field of oncology, which eventually could be exploited for personalized treatment strategies, such as patient diagnosis, prognosis and treatment purposes together with internal and external collaborators. The candidate will be expected to present their work in scientific journals and at scientific conferences.

The PhD project will be executed at the Analytical Biochemistry (AB) group. The AB consists of a dynamic, multidisciplinary group of researchers stemming from the fields of (computational) MS, proteomics and metabolomics. AB is housed in the ERIBA building at the UMCG campus and embeds the Interfaculty Mass Spectrometry Center (IMSC), which is a joint research facility of GRIP and UMCG. AB and IMSC share a well-equipped laboratory with 15 high-end mass spectrometers, primarily hyphenated with LC platforms. There is a well-equipped research infrastructure in place to perform MS-based proteomics and metabolomics, including sample preparation and handling and the analysis of MS data. AB participates in many interdisciplinary research projects, ranging from a fundamental towards a clinical perspective, with a specific focus on biomarker discovery and validation. The AB has workflows in place to enable the analysis of various omics fields such as proteomics, phosphoproteomics, lipidomics and metabolomics and investigating a wide variety of samples such as different types of cancer tissue, lung tissue, microbiological samples, blood and urine.

The PhD position will be supervised by Dr Guinevere S.M. Lageveen-Kammeijer and Prof. Peter L. Horvatovich.
For this position, we seek a highly motivated researcher with practical lab experience in the field of analytical chemistry and data analysis (or another related field). You will be responsible for your own project as well as working within a team. You will be able to manage state-of-the-art mass spectrometers and the corresponding separation platforms.

We are specifically looking for the following:

• hands-on experience with mass spectrometers, liquid chromatography or capillary electrophoresis
• affinity with both instrumental techniques and data analysis software
• MSc degree (GPA> 3.0) in Chemistry, Biochemistry or a related subject
• experience in glyco(proteo)mics is appreciated
• proficiency in English (C1 or higher)
• independent, flexible, enterprising, organized, solution-oriented
• capable of working in an interdisciplinary, academical, and international environment.

Recent illustrative work:

1. Lageveen-Kammeijer, G.S.M.*, Haan, de N.*, Mohaupt, P., Wagt, A.P., Filius, M., Nouta, J., Falck, D., Wuhrer, M. Highly Sensitive CE-ESI-MS Analysis of N-Glycans from Complex Biological Samples. Nature Communications, 2019, 10, 2137, DOI: 10.25345/C5061Z.
2. Wagt, S.*, Haan, de N.*, Wang, W., Zhang, T., Wuhrer, M., Lageveen-Kammeijer, G.S.M. N-glycan isomer differentiation by zero flow capillary electrophoresis coupled to mass spectrometry. Analytical Chemistry, 2022, DOI: 10.1021/acs.analchem.2c02840. Just accepted.
3. Kammeijer, G.S.M., Jansen, B.C., Kohler, I., Heemskerk, A.A.M., Mayboroda, O.A., Hensbergen, P.J., Schappler, J., Wuhrer, M. Sialic Acid Linkage Differentiation of Glycopeptides using Capillary Electrophoresis – Electrospray Ionization – Mass Spectrometry. Scientific Reports, 2017, 7, 3733, DOI: 10.1038/s41598-017-03838-y.
4. Kammeijer, G.S.M., Kohler, I., Jansen, B.C., Hensbergen, P.J., Mayboroda, O.A., Falck, D. Wuhrer, M. Dopant Enriched Nitrogen Gas Combined with Sheathless Capillary Electrophoresis – Electrospray Ionization – Mass Spectrometry for Improved Sensitivity and Repeatability in Glycopeptide Analysis. Analytical Chemistry, 2016, 88 (11), pp 5849-5856, DOI: 10.1021/acs. analchem.6b00479.
5. Madunić, K., Zhang, T., Mayboroda, O.A., Holst, S., Stavenhagen, K., Jin, Chunsheng, Karlsson, N.G., Lageveen-Kammeijer, G.S.M., Wuhrer, M. Colorectal cancer cell lines show striking diversity of their O-glycome reflecting the cellular differentiation phenotype. Cellular and Molecular Life Sciences, 2021, 78, pp 337-350, DOI: 10.1007/s00018-020-03504-z.

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