PhD Position in Computational Mass Spectrometry
University of Amsterdam Institute for Molecular Sciences

PhD position in Computational Mass Spectrometry

Publication date 30 March 2020

Closing date 1 June 2020

Level of education Master's degree

Hours 38 hours per week

Salary indication €2,325 to €2,972 gross per month

Vacancy number 20-217

Recent advances in analytical tools such as comprehensive two-dimensional chromatography (i.e. GCxGC and LCxLC) and high resolution mass spectrometry (HRMS) have enabled a more detailed chemical characterization of complex samples from different sources (e.g. biological and/or environmental). However, these instruments produce a huge amount of data up to 5 GB per sample. These data are highly complex and the conventional data processing approaches may not be adequate to take full advantage of the recorded information in them.

Recent technological advances in the computational sciences, including machine learning, signal processing, and cloud computing, have facilitated the handling of such data. However, the development pace of the analytical tools, so far, has been faster than the data processing ones. Consequently, there is a clear need for further development and improvement of the data analysis tools based on the advanced statistics and signal processing techniques for the detailed chemical characterization complex samples.

This project aims at utilizing the combination HRMS and modern data processing tools to facilitate the identification of natural and anthropogenic chemicals in complex samples from environmental sciences to medicinal chemistry. This project will result in an open source/access toolbox for handling such data.

What are you going to do?

You will develop new algorithms/tools or improve the existing tools within the framework of an open source package for analysis of HRMS data. The developed tools will be validated using samples from different sources, including environmental and/or biological ones. Ultimately, these tools will be implemented via a cloud system for the final deployment. All the steps taken during this project will be published as peer reviewed journal articles and will be presented in national and international conferences.

What do we require?

  • A MSc degree in chemistry or physics;
  • good knowledge of at least one high-level programing language (i.e. python3, matlab, julia, R);
  • good communication skills in oral and written English.

Advance knowledge of HRMS technique as well as latest artificial intelligence methods are appreciated.  

Our offer

A temporary contract for 38 hours per week for the duration of 4 years (initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years) and should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students. 

The salary, depending on relevant experience before the beginning of the employment contract, will be €2,325 to €2,972 (scale P) gross per month, based on a full-time contract (38 hours a week), exclusive 8 % holiday allowance and 8.3% end-of-year bonus. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Dutch Universities is applicable.

Are you curious about our extensive package of secondary employment benefits like our excellent opportunities for study and development? Then find out more about working at the Faculty of Science.

About the Faculty of Science

The Faculty of Science has a student body of around 6,500, as well as 1,600 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.

The Van't Hoff Institute for Molecular Sciences (HIMS) is one of eight institutes of the University of Amsterdam (UvA) Faculty of Science. HIMS performs internationally recognized chemistry and molecular research, curiosity driven as well as application driven. This is done in close cooperation with the chemical, flavour & food, medical and high-tech industries. Research is organised into four themes: Sustainable Chemistry, Analytical Chemistry, Computational Chemistry and Molecular Photonics.


Do you have questions about this vacancy? Or do you want to know more about our organisation? Please contact:

  • dr Saer Samanipour, Assistant professor

Job application

The UvA is an equal-opportunity employer. We prioritise diversity and are committed to creating an inclusive environment for everyone. We value a spirit of enquiry and perseverance, provide the space to keep asking questions, and promote a culture of curiosity and creativity.

Do you recognize yourself in the job profile? Then we look forward to receiving your application, a motivation letter and CV, including a list of publications, by 1 June2020. You may apply online by using the link below. #LI-DNP


If you apply for this position please say you saw it on Engineeroxy


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