Job opportunity

Current Vacancies

  • 2 PhD posiitions in Metabolomics
  • Technician
  • Postdoc position bridging Tumor Immunology and Proteomics
  • PhD position in protein Lipdation
  • PhD position in GPCR signalling

Publication date:

Feb 8th 2021

PhD Position in Chemical Biology/Protein Lipidation

Protein lipidation is the covalent attachment of lipids to proteins. Despite the important role of this fatty posttranslational modification in health and disease, knowledge about these fatty modifications is lagging behind other posttranslational modifications, such as phosphorylation and acetylation. Biomolecular mass spectrometry and proteomics seeks a highly motivated, high-potential candidate for a PhD position in a research project studying the role of protein lipidation in neurological disorders. In this project, you will work at the interface of chemistry and biology. You will contribute to the development of new chemical biology and proteomics methodologies to study the regulation of protein lipidation, focusing on S-palmitoylation, aiming to reveal how these modifications affect brain proteins, especially those that are linked to neurological disorders.

Profile
We are looking for a versatile and driven candidate, preferably with a background in chemical biology/molecular biology and who has:

  • an MSc in Chemical Biology or a related field;
  • excellent written and oral proficiency in English;
  • experience in cell culture techniques;
  • the ability and enthusiasm for working both independently and collaboratively in a highly multidisciplinary environment;
  • significant knowledge of, and experience with working in a chemical biology lab;
  • team player spirit;
  • hands-on MS experience (considered a plus, but not essential at the start).

Ideally, you also have:

  • experience in proteomics mass-spectrometry;
  • excellent writing skills.

APPLY VIA:

https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/phd-position-in-chemical-biologyproteomics-10-fte

Information

  • Position:  PhD
  • Location: Utrecht University, Utrecht, Netherlands
  • Duration: 4 years
  • Startdate: After consultation; as soon as possible
  • Background: Chemical biology, affinity purification, mass spectrometryApply with motivation letter, cv and 2 references
  • Deadline for application: 1 March 2021
  • For information or application: m.p.baggelaar@nulluu.nl; Dr. Marc P. Baggelaar

 

Publication date:

Jan 25th 2021

2 PhD positions in Metabolomics (1.0 FTE)

Metabolomics is an exciting upcoming field that studies the small molecule metabolites of the cell: the ‘metabolome’. Because metabolites are the ultimate downstream products of all biomolecular processes in the cell, different cell types – but also most diseases – are characterised by a distinct metabolic profile reflecting the specific demands that cells need to meet in order to survive or in response to their cellular environment. By studying a cell’s metabolic profile, metabolomics can give a unique view on cellular phenotypes and how these phenotypes are regulated.
The Metabolomics group of prof. dr. Celia Berkers uses state-of-the-art mass spectrometers to identify and quantify  metabolites (amino acids, sugars, lipids, nucleotides) and translate these measurements into meaningful insights in several biological systems. The laboratory is housed at division of Cell Biology, Metabolism & Cancer (Faculty of Veterinary Medicine) with close affiliations with the Biomolecular Mass Spectrometry and Proteomics group (Faculty of Science). We are currently looking for 2 candidates.

Position 1: T-cell immune-metabolism

Regulatory T cells inhibit the response of conventional T cells to self- and foreign antigens. Regulatory T cells thereby prevent autoimmune reactions, but can also impede anti-tumour immunity. The activation of regulatory and conventional T cells requires that these cells undergo changes in their metabolism. The exact mechanisms underlying such metabolic switches differ between various T-cell types and are largely unknown. By mapping metabolic differences between T cells types, novel targets for therapeutic intervention can be identified, which could benefit patients suffering from for example autoimmune diseases or cancer. 

In this collaborative project between Utrecht University and the Leiden University Medical Centre, you will combine mass spectrometry and metabolomics with immunology to study the metabolism of regulatory and conventional T cells. You will develop mass spectrometry methods to measure metabolic activities in human T cells and use these to identify targetable metabolic pathways in T cells. You will also become part of the ‘Institute for Chemical Immunology’, which brings together chemists and immunologist working across the Netherlands. You ideally have a background in metabolism or immunology. Hands-on MS experience is preferred, but not essential at the start.

Position 2: Cancer Metabolism

Changes in metabolism are increasingly regarded as one of the hallmarks of cancer cells. Malignant cells rewire multiple aspects of their metabolism to fulfil the higher demand for energy, to produce building blocks for proliferation and to maintain their redox balance. Recent studies show that metabolism is further adjusted when cells become resistant to anti-cancer therapies. Metabolism thereby offers novel entry points that can potentially be exploited to overcome drug resistance in cancer.

In this interdisciplinary project, you will bridge mass spectrometry and metabolomics with cancer biology to study how metabolic changes contribute to drug resistance in cancer. You will develop innovative metabolomics methods to study metabolism in complex in-vitro model systems such as organoids, and apply these to identify novel targetable metabolic pathways in drug-resistant tumours. You ideally have a background in metabolism or experience in working with complex in vitro models. Hands-on MS experience is preferred, but not essential at the start.

Qualifications

 We are looking for enthusiastic, highly motivated candidates, who are interested in undertaking an interdisciplinary project at the interface of Metabolomics, Metabolism and Immunology and/or Cancer Biology. You are hands-on, independent and have a passion for science.

You also have:

  • A master’s degree (or equivalent) in an appropriate discipline (e.g. Biochemistry, Biomolecular/Biomedical Sciences, Analytical Chemistry, Pharmacy/Pharmaceutical Sciences )
  • A keen interest in metabolism and metabolic reprogramming in cancer or immunology.
  • Preferably a demonstrated knowledge and experience in mass spectrometric techniques like LC-MS/MS or metabolomics.
  • Good technical skills.
  • self-initiative and you are eager to learn
  • A high level of verbal and written communication skills in English

Information

  • Position:  PhD
  • Location: Utrecht University, Utrecht, Netherlands
  • Duration: 4 years
  • Startdate: After consultation; as soon as possible
  • Background: metabolism, immunology or advanced in vitro models, metabolomics/massspectrometry
  • Please state your preference for 1 of the positions; potentially you will be considered for both.
  • Apply with motivation letter, cv and 2 references
  • Deadline for application: 15 feb 2021
  • For information or application: Celia Berkers,  c.r.berkers@nulluu.nl. 

 

Publication date:

Oct 1st 2020

Technician Analytical Biomolecular Mass Spectrometry (1.0 FTE)

Function

As our new Technician you will assist in the general research projects, with emphasis on proteomics workflows consisting of sample preparation, chromatographic separation, and MS-based characterization and quantitation of peptides and proteins. In addition, you will support the group by measuring intact native proteins with specialized mass spectrometry instrumentation, like HDX, Orbi-traps and TOF’s. Part of your time will be spent managing and running a fee for service to biopharmaceutical companies, by solving ‘research’ questions using native mass spectrometry. You will support the proteomics research by maintaining analytical equipment such as the HPLC (RP, SEC, IEX, HpH), centrifuges, etc. Furthermore, you will maintain the stock of consumables and materials and where needed assist in testing and improving the used methodology and instrumental setup.

Profile

We are looking for a hands-on, flexible, self-motivated colleague who is also a team player, open minded and creative and last but not least: you are driven by knowledge and results through your passion and enthusiasm!

You also have:

  • a Bachelor’s or Master’s in science education in analytical chemistry, biochemistry or a related field;
  • good interpersonal skills and a proven ability to communicate effectively and work well with your colleagues;
  • self-initiative and you are eager to learn and to improve current workflows;
  • the ability to follow instructions and take direction;
  • skills in using standard productivity software;
  • a demonstrated knowledge and experience in mass spectrometric techniques like LC-MS/MS, proteomics and native mass spectrometry (considered a plus);
  • experience with analytical and biochemical methods such as liquid chromatography based fractionation of peptides and proteins (considered a plus);
  • good verbal and written communication skills in Dutch and/or English and you can maintain/build good customer relations.

Offer

  • A position for 1 year with a possible extension to 3-4 years or longer;
  • A full-time gross salary ranging from €2,329 to €3,144 starting in scale 7;
  • Benefits including 8% holiday bonus and 8.3% end-of-year bonus;
  • A pension scheme, partially paid parental leave, and flexible employment conditions externe linkbased on the Collective Labour Agreement Dutch Universities (cao).

In addition to the employment conditions laid down in the cao for Dutch Universities, Utrecht University has a number of its own arrangements. For example, there are agreements on professional development, leave arrangements and sports. We also give you the opportunity to expand your terms of employment yourself via the Employment Conditions Selection Model. This is how we like to encourage you to continue to grow.

Information

  • Position:  Technician
  • Location: Utrecht University, Utrecht, Netherlands
  • Duration: 1 year with a possible extension to 3-4 years or longer
  • Startdate: After consultation; as soon as possible
  • Background: Mass Spectrometry, (LC-MS/MS, proteomics, native mass spectrometry is considered a plus). Biochemical methodology, biochemistry
  • Apply with motivation letter, cv and 2 references
  • Deadline for application: 2 dec 2020
  • For information or application: c.c.heuzer@nulluu.nl,  Corine Heuzer. 
  • Direct link to application form

 

Publication date:

Sept 3rd 2020

PhD position in protein lipidation

Signalling events between proteins, as well as protein localization, are highly and specifically regulated by the post-translational modifications (PTMs) that they can transiently harbour. Of these PTMs, phosphorylation, glycosylation and acetylation have been widely studied and characterized. Protein lipidation, the covalent attachment of a lipid group to a protein, is much less studied, but thought to be equally important. In addition to its well-established important role in fundamental biology, protein lipidation has been associated with multiple neurological diseases, including Huntington’s disease and Alzheimer’s disease.

In this project, you will work at the interface of chemistry and biology. You will develop new chemical biology and proteomics tools to study the regulation of protein lipidation, focusing on S-palmitoylation, aiming to reveal how these modifications affect brain proteins, especially those that are linked to neurological diseases. You have ideally a background in chemical biology, hands-on MS experience is preferred, but not essential at the start.

Information

  • Position:  PhD
  • Location: Utrecht University, Utrecht, Netherlands
  • Duration: 4 years
  • Startdate: After consultation; as soon as possible
  • Background: Chemical biology, affinity purification, mass spectrometry
  • Apply with motivation letter, cv and 2 references
  • Deadline for application: 31 Oct 2020
  • For information or application: m.p.baggelaar@nulluu.nl; Dr. Marc P. Baggelaar

 

Publication date:

Sept 14th 2020

Postdoc position bridging Tumor Immunology and Proteomics

Immuno-oncology is a promising new area within the field of basic, translational and clinical cancer research and recent years have seen breakthroughs where (otherwise untreatable) patients have been cured by novel immunotherapies. Immuno-oncology focusses on understanding the relationship between the tumor and the patients’ own immune system, with the aim to target the cancer or microenvironment with antibodies or immune cells. Central to this approach is the identification of unique antigens presented by the tumor cells and immunological characterization of the tumor microenvironment (TME). Mass spectrometry provides the much-needed hypothesis-free window to discovery specific and novel tumor antigens, and reveal the intricacies of the tumor immunological landscape. In this position, you will participate in the PMC-UMCU-UU tumor immunology initative, and work alongside immunologists and clinicians in joint efforts, within the strong collaborative network of the immune-oncology research community in Utrecht. A background in proteomics and tumor immunology would be appreciated.

Information

  • Position:  Postdoc
  • Location: Utrecht University, Utrecht, Netherlands
  • Duration: 3 years
  • Startdate: After consultation; as soon as possible
  • Background: Immunology, affinity purification, mass spectrometry
  • Apply with motivation letter, cv and 2 references
  • Deadline for application: 31 Oct 2020
  • For information or application: w.wu1@nulluu.nl; Dr. Wei Wu and a.j.r.heck@nulluu.nl: Prof. Dr. Albert Heck

 

Publication date:

May 4th 2020

PhD position in GPCR signalling

G Protein coupled receptors (GPCRs) are promising targets for treatment of cancer, as well as immune and inflammatory diseases. Next to small molecules, antibody therapeutics are recently found to modulate GPCR function with better specificity and longer lasting effects.

In this project, you will use combined techniques in mass spectrometry and cancer biology to study the mechanisms of novel antibody/nanobody therapeutics and bispecifics targeting GPCRs and GPCR oligomerisation. In this inter-disciplinary project bridging mass spectrometry, cell biology, and antibody/nanobody engineering, you will also become part of an extended research network collectively aimed at revealing the intricacies of GPCR signalling and rational perturbations for therapy. This ‘MAGNETIC’ consortium is funded by the NWO-ENW-PPS scheme, to develop the next-generation of GPCR-targeting pharmaceuticals. Applicants with prior knowledge in cell signalling are preferred; prior hands-on MS experience is not critical at the start.

Information

  • Position:  PhD
  • Location: Utrecht University, Utrecht, Netherlands
  • Duration: 4 years
  • Startdate: Starting in September of after consultation, as soon as possible
  • Background: Cell signaling, affinity purification, mass spectrometry
  • Apply with motivation letter, cv and 2 references
  • Deadline for application: 1st June 2020
  • For information or application: w.wu1@nulluu.nl Dr. Wei Wu

 

Publication date:

April 21st 2020

3 PostDoc positions on Epic-XS projects

 

Are you interested in developing a cutting-edge research program focused on developing and applying bioanalytical and biochemical approaches to investigate biological and disease processes?

 

General

Within the European consortium Epic-XS (https://epic-xs.eu) three different 2-year post-doctoral positions are available at Utrecht University, placed within the Heck-lab (https://hecklab.com), Altelaar-lab (https://altelaarlab.com/), and the Scheltema-lab (https://scheltemalab.com). The research emphasizes on the development of advanced mass spectrometry-based methods to address questions in proteomics and structural biology. The laboratory houses an excellent infrastructure, including a dozen state-of-the-art mass spectrometers, advanced separation technologies, bioinformatics, and laboratories for cell culture, biochemistry and molecular biology. The research group is vibrant and houses over 15 nationalities – Utrecht is a great place to be!

For all positions, the work is embedded in the European Proteomics program Epic-XS and participation in international meetings for this consortium is expected. The aim is to implement the developed technologies into the access sites, promoting collaborations.

Information

  • Position: PostDoc
  • Location: Utrecht University, Utrecht, Netherlands
  • Duration: 2 years
  • Startdate: After consultation, as soon as possible
  • Background: Experience with Proteomics Workflows, systems biology, high end proteomics  is appreciated
  • Apply with motivation letter, cv and 2 references
  • Please state preference for 1 of the positions; potentially you will be considered for multiple
  • Deadline for application: 1st June 2020
  • For information or application: c.c.heuzer@nulluu.nl

 

Position 1: Mass spectrometry driven structural investigations (https://scheltemalab.com)

The Scheltema laboratory focusses on the development and application of cross-linking mass spectrometry (XL-MS) to study protein-protein interactions. This technology utilizes small and agile reagents that covalently connect amino acids in close proximity. After proteolytic digestion, mass spectrometry can identify the connected amino acids. From these identifications distances constraints are derived that can be placed in in protein 3D structures, either known or directly predicted using this information. The structural details, at a resolution in the range of a few nanometers, allow resolving interaction interfaces between proteins. This can be done either in-vitro or in-situ in a close-to-native environment, making XL-MS an incredibly powerful approach for cell and structural biology.

For this position, you will join a team of dedicated researchers combining expertise in bioinformatics, biochemistry, mass spectrometry, and structural modeling on a variety of systems and organisms to answer cutting-edge questions in biological sciences. You are expected to apply size-exclusion chromatography and sucrose gradient ultracentrifugation to purify interesting protein assemblies, perform the cross-linking and mass spectrometry assays, perform data analysis and integrate the data into structural models. As part of the European Proteomics program Epic-XS you will interact and collaborate with international researchers and develop new methods for cross-linking mass spectrometry.

Recent illustrative work

  1. P Albanese, S Tamara, G Saracco, C Pagliano, RA Scheltema (2020) How paired PSII-LHCII supercomplexes mediate the stacking of plant thylakoid membranes unveiled by integrative structural mass-spectrometry Nature Communications 11, 1361
  2. O Klykov, C van der Zwaan, AJR Heck, AB Meijer, RA Scheltema (2020) Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling Proceedings of the National Academy of Sciences 17 (4), 1976-1987
  3. B Steigenberger, RJ Pieters, AJR Heck, RA Scheltema (2019) PhoX: An IMAC-Enrichable Cross-Linking Reagent ACS Central Science 5 (9), 1514-1522

Position 2: Clinical proteomics (https://altelaarlab.com/)

Translational proteomics has made significant progress in recent years with improved protocols for the analysis of clinically important samples such as patient biopsy tissue material and different types of liquid biopsies. The analysis of patient tissue material allows the investigation of the disease state and the treatment response directly in the native in vivo environment and thereby provides valuable molecular disease information with high translational capacity. To make translational proteomics a main technology in clinical settings, several challenges need to be addressed. Here, we will focus on tissue biopsies, as the life in vivo setting, and extracellular vesicles (EVs), which potentially contain biomarkers for diagnosis and prognosis of disease conditions. Proteomics approaches will consist of high-end shotgun proteomics and targeted proteomics (e.g. DIA and SRM).

For this position, we seek a highly motivated biochemist or analytical chemist with proven expertise in mass spectrometry and clinical proteomics. You will join a team of dedicated researchers combining expertise in biochemistry, analytical chemistry, mass spectrometry and bioinformatics on a variety of systems to answer pressing clinical questions. As part of the European Proteomics program Epic-XS you will interact and collaborate with international researchers and develop new methods to translate proteomics results in clinically relevant information.

 

Recent illustrative work

  1. Schmidlin T, Debets DO, van Gelder CAGH, Stecker KE, Rontogianni S, van den Eshof BL, Kemper K, Lips EH, van den Biggelaar M, Peeper DS, Heck AJR, Altelaar M. (2019) High-Throughput Assessment of Kinome-wide Activation States. Cell Systems 9(4):366-374.
  2. Rontogianni S, Synadaki E, Li B, Liefaard MC, Lips EH, Wesseling J, Wu W, Altelaar M. (2019) Proteomic profiling of extracellular vesicles allows for human breast cancer subtyping. Communications Biology 2:325.
  3. Zagorac I, et al. (2018) In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nature Communications 9(1), 3501.

Position 3: Native and top-down proteomics (https://hecklab.com)

In recent years we have been developing new mass analyzers and new fragmentation techniques targeted towards the direct analysis of intact proteins and protein complexes by native and top-down proteomics. Such analyses on the one hand allow us to directly probe stoichiometries and structures of large protein assemblies, like viruses and ribosome particles, on the other they make it possibly to identify and quantify distinct proteoforms of proteins highly modified by post-translational modifications such as phoshoproteins and (plasma) glycoproteins. Introducing charge detection single particle mass spectrometry and ECD and UVPD fragmentation on Orbitrap platforms has provided us with an unprecedented toolbox to discover so far little explored relevant parts of the proteome.

For this position, we seek a highly motivated biochemist or analytical chemist with proven expertise in biomolecular mass spectrometry. Having your own project, you will join a team of dedicated researchers combining expertise in bioinformatics, engineering and instrument development, biochemistry, analytical chemistry, and structural biology, and work on a variety of systems and organisms to answer cutting-edge questions in biological sciences. As part of the European Proteomics program Epic-XS you will interact and collaborate with international researchers and develop new methods for native mass spectrometry and top-down proteomics.

Recent illustrative work

  1. TP Wörner, J Snijder, A Bennett, M Agbandje-McKenna, AA Makarov, AJR Heck (2020) Resolving heterogeneous macromolecular assemblies by Orbitrap-based single-particle charge detection mass spectrometry Nature Methods 17(4), 395-398.
  2. JF Greisch, S Tamara, RA Scheltema, HWR Maxwell, RD Fagerlund, PC Fineran, S Tetter, D Hilvert, AJR Heck (2019) Expanding the mass range for UVPD-based native top-down mass spectrometry Chemical Science 10(30), 7163-7171
  3. M van de Waterbeemd, KL Fort, D Boll, M Reinhardt-Szyba, A Routh, AA Makarov, AJR Heck (2017) High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles Nature Methods 14(3), 283-286.