PhD Position in High Resolution Mass Spectrometry Anomaly Detection and Process Monitoring

Faculty/Services:  Faculty of Science
Educational level:  Master
Function type:  PhD position
Closing date:  30.01.2022
Vacancy number:  7755



Are you interested in developing new algorithms? The Analytical Chemistry Group of the Van ‘t Hoff Institute for Molecular Sciences is looking for a PhD in High Resolution Mass Spectrometry Anomaly Detection and Process Monitoring.


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.


Moreover, such data within the framework of a large environmental/biological study as well as process monitoring will result in time series. Such time series are crucial in defining the environmental and/or biological relevance of the chemical of interest. Additionally, such signals consist of noise, background, and analytical signal. However, on the fly classification of such signals remains an open question.


This project aims at developing machine learning base algorithms for the classification of the signal both withing an HRMS dataset and process monitoring time series. The developed algorithms will be employed for anomaly detection if three different case studies, from industrial to biological. 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.


You will/tasks:

  • analyse complex samples with LC-HRMS;

  • develop machine learning algorithms to detect anomalies in the signal;

  • test the developed tools in large scale case studies;

  • publish and present the findings in scientific journals and international conferences.


What do we require of you


  • MSc degree in analytical chemistry or physics;

  • working knowledge of a high level programming language (i.e. python3, matlab, julia);

  • good communication skills in oral and written English;

  • takes initiative and has good time management skills.;interest in collaborating with students and colleagues within and outside the institute

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


Our offer


A temporary contract for 38 hours per week, preferably starting in spring 2022, for the duration of four years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended to a total duration of four years). This 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 Masters students.


Based on a full-time contract (38 hours per week) the gross monthly salary will range from €2,434 in the first year to €3,111 (scale P) in the last year. This is 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.


The UvA offers excellent possibilities for further professional development and education.


What else do we offer

  • A function in which initiative is strongly valued.

  • An enthusiastic team that welcomes new members.

  • An inspiring academic and international environment in the heart of Amsterdam.


About us


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 organized into four themes: Analytical Chemistry, Computational Chemistry, Synthesis & Catalysis and Molecular Photonics.


The Analytical Chemistry Group focuses on the development of new or greatly improved techniques or methods for the analysis of complex mixtures. The technical focus is on one- and two-dimensional separation methods, on hyphenation with detection and sample-preparation systems and on chemometric techniques for data handling and optimization. The application focus is on macromolecules, forensic science and a variety of other fields.


To work at the University of Amsterdam is to work in a discerning, independent, creative, innovative and international climate characterized by an open atmosphere and a genuine engagement with the city of Amsterdam and society. Here you can read more about working at the University of Amsterdam.




Do you have any questions or do you require additional information? Please contact:



Job application


Do you recognize yourself in the job profile? Then we look forward to receiving your application by 30 January 2022. You may apply online by using the link below.


Applications in .pdf should include:

  • a curriculum vitae;

  • a letter of motivation;

  • a list of two references.


We will invite potential candidates for interviews within three weeks after the closing date.


The UvA is an equal-opportunity employer. We prioritize 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.

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