The Chair of Analytical Chemistry at University of Tartu

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.

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!

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.

Integrating omics – NPLinker workshop in Wageningen

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

Measurement Uncertainty online course: 1061 participants from 100 countries!

On Tuesday, March 25, 2025 the web course Estimation of Measurement Uncertainty in Chemical Analysis was launched the twelfth time as a MOOC (Massive Online Open Course)!

Altogether 1061 participants from 100 countries are registered – the largest number of participants the course has ever had! In the map presented above, the yellow color marks the countries form where participants come. True, the map is coarse and some countries are small. Therefore, not all countries are visible. We are very happy, that we have 9 participants also from Ukraine this year. Slava Ukraini!
Registration for this run is closed. But good news: if you did not manage to register this time, you are welcome to register for the 2026 edition of the course.

The full course material is accessible from the web page https://sisu.ut.ee/measurement/uncertainty. The course materials include videos, schemes, calculation files and numerous self-tests (among them also full-fledged measurement uncertainty calculation exercises). In order to pass the course, the registered participants have to pass six graded tests and get higher than 50% score from each of them. These tests are available to registered participants via the Moodle e-learning platform.

This course is run under the umbrella of the Estonian Center of Analytical Chemistry (https://www.akki.ee/) and forms a part of the Excellence in Analytical Chemistry (https://www.analyticalchemistry.eu/) Erasmus Mundus master’s programme.

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.

Making pH measurements in low-polarity solvents possible

For the first time, potentiometric pH measurement traceable to the conventional aqueous pH scale has been successfully demonstrated in a low-polarity solvent, 1,2-dichloroethane (1,2-DCE)!

Paulo and Jaan from our group achieved this remarkable result, which has now been published: “Experimental Unified pH Scale in 1,2-Dichloroethane” (Phys. Chem. Chem. Phys., 2025, 27, 3810–3816).

The measurement approach is rooted in the unified pH scale (pH_abs scale) concept and is based on pairwise differential potentiometric comparisons of solutions yielding their pH_abs differences (ΔpH_abs values). 85 such pair-wise measurement comparisons were carried out between solutions prepared in 1,2-DCE, some solutions in mixed solvents and aqueous standard pH buffer solutions. The resulting pH_abs “ladder” is pictured in Figure 1.

Figure 1. pH_abs scale of solutions in 1,2-DCE, linked to the standard aqueous buffer solutions and comparison against reported pHabs values in the literature.

Applying a least squares minimization approach to the ΔpH_abs values and taking into account the reference values of the aqueous standard buffers allowed us to assign pH_abs values to 19 equimolar buffer solutions in 1,2-DCE, yielding a pHabs range of −2.9 to 11.0. The consistency standard deviation of 0.17 pH units—higher than similar measurements in polar solvents—reflects the experimental challenges of working in low-polarity media.

Multiple salt bridge configurations (shown in Figure 2) were tested to improve measurement stability. Out of the four tested configurations, a separate salt bridge configuration (SB4) with PEEK capillary tubes yielded the most stable and reliable results, extending measurements for up to five hours without significant drift.

Figure 2. Different salt bridge setup configurations used in the work.

Direct pH measurement of 1,2-DCE solutions against standard aqueous pH buffers is challenging because of the very different nature of the solvents and possible water contamination of 1,2-DCE can significantly affect the measurements. Therefore, bridging solutions (a 60:40 acetonitrile/pH 4 formate solution and buffered ethanol) were employed to facilitate measurements against standard aqueous pH buffers. This approach allows the pH_abs values in 1,2-DCE to be directly comparable to the aqueous pH values.

The obtained results confirm that potentiometric pH_abs measurements are possible in low-polarity solvents, paving the way for experimentally linking many low-polarity solvents into a unified pH scale. Employing pH_abs to compare solution acidity across different media will improve our understanding of how pH impacts processes in catalysis, liquid chromatography, sustainable energy, and the interpretation of acid-base processes in various solvents.

LC-MS Validation online course 9th run has finished!

On February 14, 2025, the on-line course (MOOC) LC-MS Method Validation offered by the University of Tartu finished successfully.

Eventually, altogether 1029 people registered from 99 countries. Roughly half of them, 509 participants actually started the course (i.e. tried at least one graded test at least once) and, out of them, 299 successfully completed the course. The overall completion rate was 29%. The completion rate of participants who started the studies was 59%. The completion rates of active participants (i.e. who started the course) seems to have stabilized at around 60%, which can be considered good. In any case, there is some food for thought for us on how we could improve the overall completion rate…

At the same time, those participants who actually took part in the course were very active and asked lots of questions. The questions were often very much to the point and addressed things that are really important to analysts in their everyday work. The course has several forums (general and by topic) and during the course period the overall number of forum posts was above 300 (!) (overall number of posts, both from participants and from teachers) and the forums are still active and posts are still coming in.

This active participation made teaching this MOOC a great experience also for us, the teachers. The discussion threads gave a lot of added value to the course.

We want to thank all participants for helping to make this course a success!

We plan to repeat this course again in Autumn 2025.

Measurement Uncertainty online course: registration is now open!

The 2025 edition of the web course (MOOC) Estimation of Measurement Uncertainty in Chemical Analysis will be running from March 25 to May 7, 2025. Registration is now open!

The full course material (as well as the registration link) is accessible from the web page. The course materials include videos, schemes, calculation files, and numerous self-tests (among them also full-fledged measurement uncertainty calculation exercises) and examples. Almost all areas of analytical chemistry are addressed, ranging from simple volumetric operations and titrations to sophisticated instrumental analysis, such as determining pesticide residues by LC-MS. Efforts are made in the course to address also such uncertainty sources encountered in chemical analysis that are difficult to quantify, e.g. uncertainty due to possible interference effects (incomplete selectivity), analyte losses, etc.

In order to pass the course, the registered participants have to take six graded tests and get a higher than 50% score on every graded test. These tests are available to registered participants via the Moodle e-learning platform.

Participants who successfully pass the course will get a certificate from the University of Tartu. A digital certificate of completion is free of charge. A certificate of completion on paper can be requested for a fee of 60 euros.

You are welcome to distribute this message to potentially interested people!

Naila attending the Biodevices conference in Portugal

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.

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

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!