Indrek Saar, PhD

Indrek during his PhD defence

On the 27th of August, Indrek Saar successfully defended his great innovation-based dissertation „Development of novel on-site chemical analysis tests – from alternative materials and technologies to functional prototypes”.

With his opponent Prof. Nicole Pamme, who is focused on Lab-on-a-Chip devices, they gave a memorable and enjoyable PhD defence at the Institute of Chemistry. Prof. Nicole Pamme holds a chair in Analytical Chemistry at Stockholm University. During the defence, her excellent general science-to-market questions, as well as detailed questions specific to chemistry and material science, helped the audience to gain a clear understanding of the need for research, practical applications and how everything was also achievable from a technological perspective.

Indrek’s dissertation has given valuable new insights into the simple to use on-site chemical analysis tests.

Picture of the fully assembled Biotin test developed in this work.

What if advanced chemical testing could be done anywhere – right where the need arises, without a laboratory?

Traditional high-quality chemical analyses often require complex equipment, trained personnel, and significant time, creating a need for faster, more accessible solutions. In Indrek`s thesis, new on-site chemical analysis tests were developed that not only simplify testing but also aim to achieve higher analytical performance than existing portable methods. These tests were developed using a novel screen-printed particle-based method that is fast, low-cost, and potentially scalable for mass production.

The applications of functional prototypes included monitoring biotin levels in urine and measuring different metal cations in various water samples, even in challenging agricultural nutrient solutions containing strong chelating agents.

Separation of biotin and its metabolites on the printed microfluidics chip. The chip has been visualised by spraying it with a solution of p-dimethylaminocinnamaldehyde (p-DACA) in ethanol and sulphuric acid.

These patented innovations are laying the foundation for highly capable, mass-producible diagnostic tools that can enable faster, more accurate decision-making in environmental monitoring, healthcare, and agriculture.

During his PhD studies and research, Indrek was supervised by Dr Hanno Evard and by Prof. Ivo Leito. Indrek’s special thanks go to the main supervisor, Dr Hanno Evard, who had been a constant source of guidance, encouragement, and support. From countless discussions and brainstorming sessions to planning and problem-solving, Hanno’s insight and commitment had been central to this work.

A Smooth and Memorable Defence

Marta during her PhD defence

On the 27th of August, Marta-Lisette successfully defended her dissertation “Exploring the basicity of phosphanes and related compounds”, marking an important milestone in her academic journey. Her dissertation has given valuable new insights into the basicity and preparation of phosphanes and related compounds. The defence was conducted in an atmosphere of professionalism and collegiality, with a thoughtful exchange of ideas and perspectives.

Special thanks go to the opponent, Dr Martin Smith from Loughborough University, whose insightful and well-chosen questions guided the discussion. His role helped ensure the defence was not only rigorous but also smooth and engaging.

It was a proud moment for Marta (and her supervisors) and a wonderful occasion for everyone who has supported her throughout this process. Congratulations to her on this achievement!

From left: Ivo, Marta, Arkyn, and Agnes

Publication: Derivatization for success

Riin Rebane

Recently, a tutorial review was published in Analytica Chimica Acta by Riin Rebane and Ivo Leito, named Derivatization for success: a tutorial review of liquid chromatography mass spectrometry method optimization for determining amino compounds. Read next what Riin has to say about the review.

“This comprehensive review brings together technical depth and years of personal lab experience, shaped by long hours at the bench, countless peer discussions, and valuable lessons learned along the way. It offers a detailed, practice-oriented guide to how derivatization can dramatically improve analyte retention and ionization in LC-MS, especially for challenging amino compounds. The article dives into reagent selection, method optimization, and real-world troubleshooting – tools I wish I’d had starting out.”

This work was supported by the Estonian Research Council grant PUT1589, and by the Estonian Ministry of Education and Research (TK210). The research was conducted using the Estonian Center of Analytical Chemistry, funded by the Estonian Research Council (TT4).

Graphical abstract for the tutorial review

Paleoproteomics course by visiting Professor Matthew Collins

Prof. Collins (left) with the students demonstrating the working principles of mass spectrometry

From the 17th to the 21st of March, the Archemy group welcomed Professor Matthew Collins, a Professor of Paleoproteomics at University of Cambridge and the University of Copenhagen, at University of Tartu for a week-long paleoproteomics course.

The course, attended by students and researchers from University of Tartu and the Collège de France, covered the fundamentals, methods, and applications of ancient proteomic studies using both MALDI-TOF mass spectrometry and LC-MS/MS.

Since the attendees’ backgrounds varied from archaeologists to chemists and geneticists, the course began with a review of the fundamentals of organic chemistry. Masterfully, Prof. Collins continued with an introduction to mass spectrometry and a method called ZooMS – zooarchaeology by mass spectrometry, which is based on detecting marker peptides to determine animal taxonomy.

Students participating in the course

The course continued with an intensive introduction to analyzing the paleoproteome using LC-MS/MS and the opportunities it provides in analyzing ancient ways of life, for example, determining the species used for dairy production. However, the shortcomings of the methods were also discussed. In archaeological material, the most prevailing issues tend to be contamination with modern and more abundant proteins, as well as the deamination of amino acids due to their advanced age. Despite the difficulties in analyzing ancient proteomes, the debates on the final day still concluded that the methods are highly applicable in archaeological studies.

Prof. Matthew Collins led the intensive course within the project PaleoMIX: Nurturing Heritage Science with Novel Bioarchaeological Methods in the Eastern Baltics, PI Mari Tõrv (UT). Project partners include the University of Copenhagen, the University of Burgos, and the University of York.

Read more about paleoproteomics and its applications in an interview with Prof. Collins (in Estonian).

Unified and comparable quantification of catalytic activity of Brønsted acids is now possible!

Gleb in front of the NMR instrument

Our group’s journey into catalytic studies began years ago. In the first period our main activity was measuring the pKa values of Brønsted acids catalysts and relating them with catalytic activity. However, it was always problematic that the catalytic activity was quantified by different authors in very different ways: different reactions, different substrates of the same reaction, different ways to express activity (rate constant, yield), different solvents, different concentrations, different temperatures… All this diversity makes comparing catalytic activity difficult to impossible.

So, we set forth to find a model reaction, define conditions and a unified quantitative parameter for expressing acatlytic activity of various Brønsted acid catalysts.

This endeavour has now reached its first result: PhD student gleb Maksimov from our group discovered that the transfer hydrogenation reaction with substituted quinoline has the suitable characteristics for this work and utilizing the Kimball-Collins theory modelling approach applied to rate constante (measured by NMR), a catalytic activity parameter was defined that enables unified and comparable quantification of the catalytic activity of Brønsted acids! The proof of principle is now published: Molecular Catalysis 2025, 573, 114846. Towards quantifying catalytic activity of homogeneous Brønsted acid catalysts.

Congratulatuons, Gleb!

However, this work is far from complete. Gleb together with new students will continue to improving te methodolog and widening the applicability of the approach so that many more results and with higher quantitative accuracy would be possible in the future. We are excited about the potential advancements and look forward to sharing more updates as the research progresses.

(This research was supported by grant PRG690 from the Estonian Research Council)

 

Integrating omics – NPLinker workshop in Wageningen

Pilleriin in front of her poster

They say it takes a village to raise a child—and in science, it takes a community to push boundaries and do great science. In the multi-omics field, the best discoveries emerge from collaboration among chemists, microbiologists, bioinformaticians, computer scientists, and many others.

The NPLinker community in Wageningen, Netherlands, is dedicated to bridging the gap between genomics and metabolomics while also connecting researchers analyzing these complex datasets.

This week Pilleriin Peets had the fantastic opportunity to once again participate in their five-day intensive hands-on workshop, which covered key tools and applications, including BiG-SCAPE, MZmine, GNPS2, NPLinker, and PairedOmics.

A highlight of the week was the Symposium on March 26, celebrating 10 years of genomics mining and 5 years of metabolomics mining at Wageningen University & Research. Genomics mining research in Wageningen is led by Marnix Medema, whose developments include antiSMASH and MIBiG. Metabolomics topics were covered by Justin J.J. van der Hooft, whose contributions to the field include PairedOmics platform, as well as MS2Query.

The symposium’s keynote was delivered by Pieter Dorrestein, one of the most influential scientists in metabolomics, with over 400 publications and 75,000 citations. His work in computational metabolomics includes the Global Natural Products Social Molecular Networking (GNPS) platform, which enables researchers to find spectral connections within their samples and annotate compounds using publicly available spectra. During his talk, he highlighted his bile acid research and emphasized the critical role of open-access data in advancing the field.

Knowledge from this week will be brought back to Tartu and Pilleriin is eager to integrate GNPS2 into her workflow to enhance compound annotation in her non-targeted mass spectrometry datasets.

Pieter Dorrestein and Justin J.J. van der Hooft

The Cultural Heritage research group published an article about their novel developed laser ablation-based analytical system (LA-APCI-MS) capabilities!

Within the framework of the PRG1198 research project Dr Signe Vahur with her team (Dr Anu Teearu, Dr Rünno Lõhmus, Martin Leissoo, Dr Alexey Treshchalov, Dr Janis Lungevics, Dr Georg Arju, Dr Hilkka Hiiop) has published a new article titled “Characterisation of laser-ablated craters of different painting materials and evaluation with modified LA-APCI-MS system” in the Journal of Talanta. The article is available here: https://doi.org/10.1016/j.talanta.2025.127856

The article presents preliminary results obtained by investigating the pulsed 355 nm Nd:YAG laser’s impact on specific painting materials (oil and acrylic paints and varnish) surfaces by characterising the area and volume of laser-ablated craters (measured with an optical microscope and 3D profilometer) obtained with different laser energies and the number of pulses at 90°, 70°, and 45° incidence angles and evaluating intensity of corresponding MS signals obtained with APCI-MS.

Naila attending the Biodevices conference in Portugal

Naila next to her poster

From 20-22 February, Naila attended the 18th International Joint Conference on Biomedical Engineering Systems and Technologies (BIODEVICES2025) in Porto, Portugal.

Biodevices conference was part of a joint conference (BIOSTEC) that covered different topics such as electronics, microfluidics systems, and biodevices and brought together scientists from various backgrounds worldwide. It was exciting to listen to presentations about new achievements in different areas related to biology and medicine. Topics varied from monitoring and diagnostics devices, sensors, and instrumentation systems to wearable and implantable devices. 
 
It was her first international conference, and she had the pleasure of sharing her science in a poster presentation format. The poster was based on the article that she is working on titled “Alkaline phosphatase-based ELISA and particle-based microfluidic test for biotin detection.” She enjoyed inspiring and challenging discussions with her colleagues from diverse scientific backgrounds and checking other posters by her colleagues. 
 
Besides, she commented on how fascinating the conference venue, a coastal city of Portugal, Porto, was with its colourful buildings, calming riverside, kind people, and warm weather. It was a perfect mix of cultural and scientific experience as her first international adventure.

Professor Hilkka Hiiop was elected as the rector of the Estonian Academy of Arts

Professor Hilkka Hiiop

On January 31, 2025, Professor Hilkka Hiiop was elected as the next rector of the Estonian Academy of Arts (EKA). Hilkka has been the Dean of the Faculty of Art and Culture since 2021 and the leading force in the Department of Cultural Heritage and Conservation for more than 10 years. Since 2021, she has also been a member of the PRG 1198 project working on the development of the laser-pen probe-MS system.

Hilkka has led numerous award-winning projects, the most recent one being the recovery and restoration of the Plafond painting in the Estonian Knighthood House. In this project, assoc. prof. Signe Vahur from our chair was also involved in performing the analysis of numerous samples to help identify the materials used in this rare work of art.

For more on Hilkka, our collaboration, and the magnificent plafond, see here (in Estonian): https://jupiter.err.ee/1609565348/eesti-lood

Congratulations, Hilkka! We wish you strength and success in your new position!

Something is “cooking”

Bettany Hughes (on the right) talking with Mari

The world-famous historian and broadcaster Bettany Hughes was back in Estonia last week, and this time she visited scientists at the University of Tartu, including the members of the Archemy Lab from our chair of analytical chemistry. Ester and Mari talked about their interdisciplinary research and recent discoveries in biomolecular archaeology.

As they say in the filming industry “to be continued…”.

Below are some first shots of the filming with Ester. 

Photos by Kätlin Jansons