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

Mari Tõrv – recipient of the Baltic Women in Science fellowship

We are happy to announce that a member of our group, Mari Tõrv, research fellow in the Archemy team, is one of the three Estonian researchers to receive the Baltic Women in Science fellowship this year!

From left: Mari Tõrv, Kadri-Ann Pankratov and Marju Himma (photos by Martin Mae)

Mari’s research delves into the biological and cultural diversity of ancient humans, emphasizing the duality of the human body as both a historical and cultural construct and a biological reality. She studies life and death in past cultures through the analysis of ancient human remains, highlighting the importance of understanding end-of-life rituals to fully grasp human nature, a subject often taboo in the Western world.

Tarmo Soomere, President of the Estonian Academy of Sciences emphasized “Talented and successful women scientists deserve to be highlighted and recognised across the whole spectrum of science. Their example inspires and ignites.”

The fellowships were funded by the Ministry of Education and Research and awarded within the program co-organised by the Baltic National Academies of Sciences and National Commissions for UNESCO. The fellowship is aimed to support the research of young women scientists to continue their outstanding work in the Baltic States. 

See the video below, where Mari talks more about her research. The basis of this blog post and information on the work of the other two laureates can be found here

Chemicum 15 – pH Cookie Cake!

On the 23rd of October, the building that has been the home to the Institute of Chemistry of the University of Tartu – Chemicum – turned 15 years old!

To celebrate the special occasion, all the Chairs of the Institute prepared various dishes showcasing some of their research fields. Of course, our Chair of Analytical Chemistry was also present with a special cake – a pH cookie cake!

The cookie cake was 100 x 40 cm large and consisted of classical layers of whipped cream mixed with curd, chopped bananas and cookies.

The main attraction was the decorative top layer, where we used colourful fruits and berries to visualise the pH and pKa scale with the typical colour gradient.

In addition, some structures of acids and bases made from chocolate were added as representative examples.

The making of the cake turned out to be a fun group activity, which is best seen in the gallery below.

The making of the cake turned out to be a fun group activity, which is best seen in the gallery below (or click here for the full gallery).

Happy birthday, Chemicum!

Ester Oras was selected as the Femal Academic of the Year!

We are happy to announce that Ester Oras, Associate Professor in our Analytical Chemistry Chair and PI of the Archemy group has received the honorary title “Female Academic of the Year” from the Estonian Association of Academic Women

Ester Oras. Photo: Andres Tennus

Ester is a modern scientist who works across multiple disciplines, integrating methods from archaeology, chemistry, biology, and even food science. Her research is primarily focused on ancient diets in Northern Europe, particularly in Estonia. Through this work, she established the first archaeochemistry lab in the Baltic region called “Archemy” at the Univeristy of Tartu. Her studies focus on ancient food practices — what people ate, how diets varied between social classes, and how food was tied to broader economic and cultural systems. She has also applied her expertise in archaeochemistry to investigate topics such as ancient migrations and Stone Age crafting technologies.

At the same time, Ester’s research extends well beyond Estonia. She has trained at leading research institutions worldwide, including Oxford, Cambridge, Max Planck Institute, and Weizmann Institute, mastering advanced analytical techniques like mass spectrometry and chromatography. Internationally regarded as an expert in the biomolecular analysis of food remains, she collaborates with researchers from countries like Germany, Finland, and the UK. Her work has been published in over 50 scientific articles across top journals in archaeology and natural sciences. In recognition of her groundbreaking research, she was recently awarded the prestigious ERC Starting Grant, and she holds several international leadership roles in organizations such as the International Society for Biomolecular Archaeology.

Beyond her scientific work, Ester is deeply committed to public outreach and gender equality in science. She regularly speaks at schools, museums, and on television, raising awareness about archaeology and inspiring future generations of scientists. She is an advocate for women in science, having launched also in Estonia the celebration of the International Day of Women and Girls in Science and contributing to numerous international gender equality projects. Her leadership extends to the University of Tartu, where she has been part of developing the university’s gender equality plan and growing a more inclusive academic environment. Through her interdisciplinary research, international collaborations, and dedication to social issues, Ester is shaping both the future of science and the role of scientists in society.

Congratulations on this well-deserved recognition, Ester!