Vacancy Postdoc 'Real-time glycopeptide identification software for glycoproteomics'

Job description

We are looking for a postdoc in informatics/chemometrics to develop analytical solutions for interpretation of glycopeptide fragmentation mass spectra in glycoproteomics. This project is a continuation of our Translational Metabolic Laboratory (TML) - Bruker Daltonics (BDAL) collaboration to develop software for real-time glycoproteomics data processing to, ultimately, advance patient care by unlocking large-scale site-specific glycobiology information. Are you the highly motivated and enthusiastic postdoc to help us with this project? We would like to get to know you!

You will develop tools based on graph theory for database-free glycan topology identification from MS/MS data. Technology will be developed based on and implemented in a recently introduced glycoproteomics software, “GlycoScape”, in the “Myriad” workflow for real-time de novo glycopeptide identification (doi: 10.3390/ijms24097869). In addition, real-time glycopeptide identification capabilities will be exploited to enable on-the-fly adjustment of data acquisition decisions and parameters to enhance glycoproteome coverage.  

With the GlycoScape - Myriad project, TML and BDAL follow an open innovation approach: while the code of Myriad is and will stay public, GlycoScape is a proprietary integrated version of Myriad. This allows external developers from the open-source community to contribute to future versions of Myriad, while the integration and optimization for the real-time analysis for timsTOF instrumentations will stay proprietary.

You will be part of our glycoproteomics team composed of experts from TML and BDAL in mass spectrometry, (bio)informatics, software/hardware engineering, and glycoscience. The position is formally housed within the (glyco)proteomics team of TML where technology innovations by the post-doc will be developed. As this position is at the heart of our public-private partnership, regular international project meetings will be held with project members. You will have direct access to code repositories and support from application and R&D experts of both partners during this project. 

Tasks and responsibilities

• Develop real-time glycan topology identification algorithm based on proof-of-concept data using graph theory.
• Develop functions to direct data acquisition decisions and parameters based on real-time glycopeptide identification results when measuring. 
• Disseminate results via scientific publications and presentations at scientific meetings.
• Share results and align technical developments with TML and BDAL experts.

Place of work

As a post-doc you will be working within the Joint Center of Excellence for Translational Omics established among Radboud University Medical Center (RUMC) and Bruker Daltonics (BDAL) and will be physically based in the Translational Metabolic Laboratory (TML) of the department of Human Genetics at the RUMC.

Translational Metabolic Laboratory 
TML is an ambitious mixed function laboratory with a focus on translational research and diagnostics for patient care. We harbor a range of top scientists in the areas of inherited (metabolic) diseases, mitochondrial disease, glycosylation disorders and more. Translational functional Omics technologies are applied at TML to develop novel personalized diagnostics. TML houses a broad range of mass spectrometry equipment including the latest generation trapped ion mobility spectrometry – quadrupole time-of-flight tandem mass spectrometry instruments (timsTOF Pro) connected online to GPU-powered real-time data processing hardware (ProteoScape/GlycoScape) and cloud-based computing infrastructure (Digital Research Environment). We coordinate the Radboud Technology Center for Mass Spectrometry and several large national and European projects including the Netherlands X-omics Initiative. There is a visual impression of TML available.  

Bruker Daltonics
Bruker is enabling scientists to make breakthrough discoveries and develop new applications of mass spectrometry that improve the quality of human life. Bruker’s high-performance scientific instruments and high-value analytical solutions enable scientists to explore life- and materials- science questions at spatial biology, cellular, subcellular and molecular levels.

Radboudumc
Welcome to Radboud university medical center (Radboudumc), where our research groups strive for innovative solutions that make impact on health and healthcare. We challenge the status quo to overcome current and future health challenges. Our goal is to shape the future of healthcare for generations to come. Our focus is on prevention, sustainability, and meaningful care, which we achieve through our in-depth understanding of disease mechanisms, clinical science, public health research, medical technology and data science. Our approach is centered on breakthroughs that can truly enhance personalized healthcare and public health. 

At Radboudumc, a comprehensive range of research programs provide the compass for our research efforts. Each program has a clear goal, where collaboration within and outside our organization is highly valued. We integrate care, education and research in partnership with our patients to ensure that our research programs have significant impact on health and healthcare. We invite you to join us in our mission to create a healthy future for all.

Profile

You hold an academic degree (PhD) in informatics or chemometrics, preferably with a background in mass spectrometry-based Omics technology. You possess excellent oral and written communication skills and have the capacity to communicate high-level expert knowledge at different levels with team members active in various scientific fields. Additionally, you are proactive and enthusiastic, making you a valuable asset to our team.

Employment conditions

At Radboud university medical center, you build on your future. We are committed to providing the best care, education, and research. And we are true to our word, because we help you develop and seize opportunities and give you the room to grow. As an employer, we believe that employees should feel vital and happy at work in all stages of life. We are also committed to creating a healthy and safe working environment. Our employment conditions contribute to that. What we offer:

• A gross monthly salary between € 3.493 and € 5.504 (scale 10) for full-time employment (36 hours per week). You will also receive an 8% holiday allowance, an 8.3% end-of-year bonus, and, depending on the position, an allowance of 47% to 72% for working irregular hours.
• 172 vacation hours per year based on a 36-hour working week. (As of 1 January 2025, you will receive 176 vacation hours).

And there is more..

• An Employment Conditions Selection Model, allowing you to use part of your employment conditions to your choosing. For example, you can use your gross salary to purchase additional vacation hours or hours for providing informal caregiving. Or, for example, you can use your gross end-of-year bonus to purchase a bicycle, so you pay less tax.
• Plenty of opportunities for personal development. You can take a variety of courses in our online learning environment. 
• Your well-being and vitality are a priority. For example:
  • Save time for work-life balance leave. 
  • You can enjoy unlimited access to a variety of activities five days a month and take advantage of all the facilities at Radboud Sport & Culture for only €27.05 per month (instead of €41)
  • Healthy Professionals program to help you manage your energy. 
  • Company Support Team and a personal coach if you are going through a life-changing event.
  • Financially beneficial working less through a Generation Scheme as you approach state pension age.
• Support in achieving a good work-life balance at every stage of your life. Examples:
  • Advice and courses on, for example, 'Millennial dilemmas' and 'Your Career After 57'.
  • Activities at our own mindfulness center.
  • Informal caregiving consultations if you have questions about juggling work and caregiving responsibilities at home.
• In addition to statutory pregnancy and maternity leave, Radboud university medical center offers 26 weeks of parental leave, nine of which are paid. In addition, as a partner you can take a maximum of five weeks of supplementary partner leave. During supplementary partner leave and parental leave, we supplement the UWV benefit up to 100% of your salary.
• Pension accrual at the ABP Pension Fund. Radboud university medical center pays 70% of the pension premium. 
• Discounts on supplementary packages of two group health insurances and ten other types of insurance, from home insurance to legal assistance.
• An allowance for your commuting costs of € 0.18 per km up to a maximum of 40 km one way. If you use public transport to commute, we will fully reimburse the public transport costs (2nd class). If you regularly work from home, you will receive a working from home allowance of € 2.35 per day.

Application procedure

Are you ready to think further for our patients and our care? We would like to receive your application before 8 November 2024. We will then contact you shortly.

Good to know

• This position requires a Certificate of Conduct (VOG).
• You can find more information about our application procedure and frequently asked questions on our website.
• Will you be our new colleague? Then you will be given the time and space to get to know your role, your workplace, and your colleagues. An induction day for all new colleagues is an integral part of your onboarding program. 

We are recruiting for this position ourselves. Unsolicited marketing is not appreciated, but do feel free to share the vacancy in your network!

Contact

Any questions? Or wondering what it is like to work at Radboudumc? Then call or email to Hans Wessels, senior researcher, through (024) 361 63 97. Use the Apply button to submit your application.