Department Environmental Chemistry

Open master thesis topics 2021

Development and application of an IC-HRMS/MS method to study very polar and ionic pesticides in karst groundwater

Possible starting date: From mid September 2021


Among the wide range of anthropogenic substances found in the environment there are potentially harmful, very polar and ionic substances which are mobile in aquatic systems. These substances include industrial chemicals, pharmaceuticals and plant protection products. Additionally, transformation products (TP’-s) of these compounds are found in aqueous environmental samples. TP’­‑s are often times more polar than their parent molecules and thus are more mobile in the aqueous environment. The discussion around very polar and ionic compounds intensified in the last few years and hence, adequate analytical techniques to cover such compounds are needed. By using e.g. traditional reversed-phase liquid chromatography, we often fail to detect very polar and ionic compounds (i.e. gap compounds).

Study goal:

In this study, we want to focus on very polar and ANionic pesticides and their very polar and anionic TP’s. We aim to develop an ion-chromatographic method to close the “analytical gap” and screen for these compounds in environmental samples. Establishing this method in our institute enables us to study very polar and anionic compounds in many different fields of water research. In a first application, we want to use this method in the analysis of temporally highly resolved karst groundwater samples from the Swiss Jura to study the pollutant dynamics of very polar and anionic pesticides in such vulnerable aquatic systems. Our preliminary results on nitrate and previous studies in the literature indicate that negatively charged ions are very mobile in karstic groundwater. This could also hold true for very polar and anionic pesticides and their very polar and anionic TP’s.


The student will gain skills in working with analytical techniques in general and in particular ion-chromatography (IC). More specifically, the student will:

Optimize the IC-method such that: a) low LOQ’s are reached for a broad spectrum of substances, b) ion-suppression through inorganic salt-ions is reduced, c) chromatographic run-times are improved

Use this method to analyze temporally highly resolved samples taken in a karstic spring after a rain event.

Supervised by Johannes Schorr, 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: as soon as possible

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) are the methods of choice to reach a sufficient abatement of micropollutants. However, the application of granular activated carbon (GAC) and the combination of ozonation with activated carbon treatment are currently under investigation to evaluate their potential to fulfill the requirements of the new water protection act.

Within the context of the SCREEN-O3TP project, samples have been collected from three WWTPs with GAC and PAC treatment, with and without a pre-treatment with ozone. The aim of this master’s thesis is to quantify the abatement of known micropollutants during advanced wastewater treatment and compare these efficiencies among the different study locations. Also known ozonation transformation products will be evaluated for their fate in GAC and PAC post-treatments. The student will learn how to conduct a quantitative target and qualitative suspect screening for measurement acquired with liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). He/she will also become acquainted with up-to-date wastewater treatment technologies applied in full scale in Swiss WWTPs. Since all measurements are already done, this master thesis does not involve lab work, but insight can be gained.

Keywords: LC-HRMS, advanced wastewater treatment, target and suspect screening, ozonation transformation products

Supervisors: Christa McArdell & Jennifer Schollee

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 (

Pollution fingerprint of waste water – development of a novel combinatory approach linking LC-ICP-MS and LC-Orbitrap

Starting date:  as soon as possible

keywords: LC-HRMS, LC-ICPMS, non-target screening, industrial and municipal wastewater

LC-Orbitrap-MS is a powerful tool to analyze micropollutants in environmental samples such as wastewater effluent. However, it is often difficult to pinpoint to the most environmentally important signal. Through combination with ICP-MS-MS one could obtain further information on the content and distribution of the elements S, Br, Cl and I, which are often associated with high toxicity. This valuable information is then used to prioritize and identify novel emerging contaminants.

In this Masterthesis we aim to combine ICP-MS and Orbitrap MS by developing a suitable mobile LC-system and optimization of both mass spectrometry methods. The established method will be applied to industrial wastewater to locate polluted hotspots and identify novel contaminants of concern.

We encourage Students with a strong background in analytical chemistry or some experience with one of the two mass spectrometers to apply. During your time at EAWAG you will get hands on experience on two cutting-edge mass spectrometers (Orbitrap and ICP-MS/MS) and learn valuable skills of data analysis and in depth understanding of high resolution mass spectrometry and its potential for structure elucidation.

Key Tasks:

  • Method development and independent hands-on experience on ICP-MS and LC-Orbitrap-MS, two state of the art powerful mass spectrometers
  • Application to real samples from an industrial wastewater treatment plant
  • Identification of chromatographic hot spots and structure elucidation of interesting peaks by high-resolution tandem mass spectrometry