Department Environmental Chemistry

Open master thesis topics 2022/2023

Identification of Human Synthetic Antioxidant Metabolites in Wastewater

Possible starting date: February 2023 or later


Synthetic antioxidants (SAOs) are chemicals of emerging concern, since they are ubiquitously present in everyday life products, such as plastics. With the outbreak of the Covid-19 pandemic, they are of even more interest, as they are contained in facemasks. Consequently, it is expected that human take them up. Upon entrance into the human body, metabolization is expected, in order to increase their polarity and to enhance their excretion. After excretion, they end up in wastewater treatment plants, whose wastewater can be analyzed after sample preparation with high-performance liquid chromatography coupled to high resolution tandem mass spectrometry (HPLC-HRMS/MS).

As their name says, SAOs possess antioxidant characteristics, as they can undergo reactions with radicals, to prevent oxidation of the product they protect. The resulting oxidized products may be identical to the human metabolites, as many biotransformation reactions are of oxidative nature. The aim of this project is to identify human metabolites of SAOs in wastewater water and thereby indirectly human exposure. In a second step, the goal is to develop an experiment to identify oxidation products of these compounds in order to ensure that the identified metabolites exclusively originate from human metabolism.

This project will start with a data analysis part of previously acquired HPLC-HRMS/MS data on wastewater samples. Several software tools will be used for screening SAO. The results will be used in the second part to design and execute an experiment for the identification of oxidized products followed by hands on HPLC-HRMS/MS measurements.

We are looking for a chemistry or environmental science student with some background in biogeochemistry or any other natural science student with some laboratory experience and who is motivated to learn more about environmental chemistry. The start of the project is flexible. If you are interested, please contact

Corina Meyer or

Prof. Dr. Juliane Hollender


Comprehensive evaluation of organofluorine chemicals in wastewater with high-resolution mass spectrometry

Possible starting date: January/February 2023, but an earlier starting date could be discussed


The presence of fluorine-containing chemicals in the aquatic environment is of increasing concern, due to their stability and potential impact to organisms in receiving waters and drinking water resources downstream of wastewater treatment plants (WWTPs). Per- and polyfluoroalkyl substances (PFAS) include many compounds with different chain length and functional groups, and are used in industry and different consumer products like textiles, electronics, coatings, and fire fighting foams. Beside the PFAS, organofluorine compounds, which include fluorine-containing pharmaceuticals and pesticides, also contribute to the total fluorine content. However, little is known about their relative importance or fraction.  

In this project we want to evaluate the occurrence and contribution of the organofluorine compounds in wastewater by screening for characteristic MS2 fragments to find known and suspected compounds, but also transformation products of them.  Influents and effluents of WWTP will be sampled and analyzed with liquid chromatography coupled to high resolution mass spectrometry (HRMS).

We are looking for a person with a background in chemical analysis and with interest in programming (scripting with R).

Keywords: LC-HRMS, organofluorine micropollutants, programming

Supervisors: Christa McArdell, Heinz Singer & Kathrin Fenner.


Elucidation of toxicity components in wastewater by integration of HRMS analysis and data mining

Possible starting date: From mid September 2022


With the development of high-resolution mass spectrometry and nontargeted screening workflows, we are able to detect and process tends of thousands of unknown and potentially harmful environmental pollutants in aquatic samples. However, since even the most sophisticated data analytics workflows require manual verification for tentative identification and quantification, we have to prioritize which compounds are most relevant in different studies. Such prioritization strategies are often based on the measured areas or frequencies of occurrence, both of which lack toxicological relevance so critical in the context of environmental pollution. In order to append toxicological relevance to HRMS analysis, machine learning methods (ML) are being developed to predict the toxicity of unknown features based on their MSMS spectra and thus prioritize the compounds based on their potential toxic effect. 

Study goal:

In this study, we want to focus on the analytical validation of MLinvitroTox, an ML tool under development at Eawag for the prediction of toxicity fingerprints for unknown HRMS features based on their MSMS spectra. We aim to deploy MLinvitroTox on wastewater samples for prioritization of potentially toxic species towards tentative identification and quantification, followed by confirmation/rejection with authentic standards. In this work, we will collect and analyze wastewater samples as well as use the “digitally frozen” sample repository already present at Eawag. This work will help to establish the validity of the proposed approach as part of the EXPECTmine project (Mining toxicity and HRMS data for linking exposures to Effects: 


The student will gain skills in working with analytical techniques in general and in particular ultra-high-performance liquid chromatography-tandem high-resolution mass spectrometry (UHPLC-HRMS/MS). More specifically, the student supported by the supervisor will collect and analyze wastewater samples, perform targeted, suspect, as well as nontargeted analyses, deploy MLinvitroTox on the results, identify potentially toxic features of interest, and attempt to confirm their identity analytically. The work will combine fieldwork, analytics, machine learning, and cheminformatics.
Supervised by Dr. Kasia Arturi, Prof. Dr. Juliane Hollender.



Environmental behavior and analytical chemistry of natural toxins

Starting date to be discussed

Natural toxins present a threat to water quality. Those from cyanobacteria are directly released into the surface waters when the cells die. Cyanobacterial blooms are increasing in frequency and intensity also related to climate change. The World Health Organization recognises few liver toxins and neurotoxins produced by cyanobacteria. But more than 2000 bioactive metabolites from cyanobacteria are known to date. Why have we not studied them yet? Only 1% of these compounds are commercially available, which makes it very challenging to study them. We work with laboratory cultures and field samples of cyanobacteria to develop analytical tools, assess photochemical and biotransformation and conduct monitoring in Swiss lakes. We are interested in prioritizing abundant and persistent metabolites to then study their abatement during drinking water treatment and their toxicological and ecological roles.

Within this topic we have several opportunities for a Master thesis for example on:

  1. Environmental fate processes of cyanotoxins
  2. Analytical tools to identify cyanopeptides by mass spectrometry
  3. Cyanotoxins and bioactive metabolites in Swiss Lakes

The common aims of these projects are to become familiar with the world of cyanopeptides and to gain experience identifying metabolites by mass spectrometry.

Depending on the specific focus of each project, you will also learn how to set up and run photochemical or biotransformation experiments to assess half-lives of cyanopeptide under simulated environmental conditions. The more analytical oriented projects will dive deeper into the identification of cyanopeptides by analyzing measured and predicted mass spectra by various software tools, which are the analytical fingerprint of a molecule. The field-related projects would entail to explore data from the past years of Swiss lake campaigns and to join ongoing sampling to monitor cyanotoxins in our surface waters.

For a successful thesis, you should 

  • have strong interest in environmental and analytical chemistry
  • have first experience (practical courses, internships) regarding laboratory work
  • be proficient in speaking and writing in English
  • be enthusiastic and motivated

Keywords: cyanobacteria, toxins, mass spectrometry, photochemistry

Advisors: Dr. Elisabeth (Lilli) Janssen

Please contact:

Evaluation of organic micropollutant abatement in advanced wastewater treatment

Starting date: to be discussed

Short description:

The presence of micropollutants in treated wastewater is of increasing concern, due to their release and potential impacts to organisms in receiving waters and drinking water resources downstream of wastewater treatment plants (WWTPs). The new Swiss water protection act implemented as of January 2016 aims at reducing the concentrations of these compounds through advanced wastewater treatment. Ozonation and treatment with powdered activated carbon (PAC) were originally the methods of choice to reach a sufficient abatement of micropollutants. The application of granular activated carbon (GAC) filtration and the combination of ozonation with activated carbon treatment were only recently evaluated and can also fulfill the requirements of the new water protection act. Installation of advanced wastewater treatment is successfully ongoing, however, there are open questions regarding the abatement of micropollutants during GAC filtration, the use of sustainable PAC materials, and also on the formation of ozonation transformation products (OTPs) and their abatement during post-treatment with GAC or sand filtration.

In the master thesis, LC-MS/MS (TripleQuad or high-resolution mass spectrometry) measurements either on target micropollutants or on suspect OTPs will be done to answer specific open questions. This is an interdisciplinary project in the two departments environmental chemistry & process engineering. Contact us if you are interested in this project and have a background on environmental chemical analysis.

Keywords: LC-MS/MS, advanced wastewater treatment

Supervisors: Christa McArdell, Marc Böhler

Does enzyme evolution generated through changes of substrate specificity induce different O2 activation pathways

Preferred start date: Summer 2021

Short Description:

The faulty oxygenation of xenobiotic compounds leads to the formation of reactive oxygen species (ROS) after O2 activation. Those ROS are thought to promote mutations that ultimately lead to the adaptation of exposed microorganisms and their enzymatic machinery to new carbon sources. In this master thesis we will test this hypothesis by assessing several biochemical indicators for O2 activation and substrate specificity using a microbial strain that has evolved through a substrate adaption processes.

To that end, we will work with Acidovorax sp. strain JS42 as well as mutant strains which were generated by switching from 2-nitrotoluene to 3-nitrotoluene as source of carbon and energy. This selection process has led to enzymes with enhanced affinity for the new substrate compared to the wild type enzyme. While mutations are documented by changes in amino acid residues, information on the efficiency of substrate oxygenation, O2 uncoupling, and the type of activated O2 species are lacking and will be provided in this work. 

Links: Project flyier (; Group webpage (

Supervision: Thomas Hofstetter (, Charlotte Bopp (