New Publication: Determination of pKa values of fluorocompounds in water using 19F NMR

Our group is well-known for pKa measurements in different solvents. So far, mostly UV-Vis spectrophotometric method has been used. Recently Elisabeth Parman (on the photo) from our group has been developing a method for measuring pKa values of fluorocompounds, using 19F NMR. NMR measurements to determine pKa values have several advantages compared to UV-Vis spectrophotometry. For example, accurate concentrations are not needed, the method is much more tolerant to impurities and several compounds can be measured simultaneously. The newly developed method has now been published in the Journal of Physical Organic Chemistry: Determination of pKa values of fluorocompounds in water using 19F NMR by E. Parman, L. Toom, S. Selberg and I. Leito.
In this work, the developed method was applied to 19 fluorocompounds – fluorinated phenols, carboxylic acids and sulfonamides, hexafluoroisopropanol (HFIP), perfluoropinacol, etc – with the aim of determining their pKa values in water, in the range from about 3.5 to 10. Several advantages of the 19F NMR method were demonstrated in pKa measurement. In particular, using multiple relative measurements against several reference compounds with known acidities it is possible to obtain highly reliable pKa values. Elisabeth convincingly demonstrated that the literature pKa values of two of the investigated compounds were inaccurate and provided more reliable values for them.

Optimization of flow splitting and make‐up flow conditions in liquid chromatography/electrospray ionization mass spectrometry

The measured ionization efficiencies in different solvent systems. The colour of the box plot background shows the organic modifier (90%): Green – Methanol, blue – Acetonitrile, red – Acetone, orange – Isopropanol. The letter shows the water phase additive (10 mM): F – Formic acid, O – Oxalic acid, P – Propionic acid

Recently a study in Rapid Communications in Mass Spectrometry was published. In this study, we optimized the actual split ratio and make-up flow composition in LC/ESI/MS analysis to increase the signal in radio detector and enhance the sensitivity of electrospray ionization.

High methanol content increases electrospray ionization efficiency

We studied make-up flow composition with a set of 20 pharmaceuticals covering 21 different make-up flow compositions. We studied methanol, acetonitrile, isopropanol and acetone as organic modifiers. As we studied positive mode the acidic additives under investigation were formic acid, oxalic acid and propionic acid. DMSO and sulfolane as additives were studied as well. The Methanol/10 mM formic acid in water (90/10) proved to be the best make‐up flow composition in relation to the average sensitivity obtained. Stronger acidic conditions using oxalic acid or higher formic acid concentrations had a clear positive effect on the sensitivity of compounds with low ionization efficiency.

Split-ratios remain stable over main part of the gradient

The second part of this study was testing and monitoring different split ratios (1:10, 1:100 and 1:250) with different splitters (Alliance flow‐splitter kit and homemade T-piece splitter). To monitor the actual split ratio haloperidol solution was added with infusion pump post-column while a haloperidol-d4 solution was added as a make‐up flow by the ISM pump after the splitter. The tested split ratios were relatively stable over the main part of the gradient but showed some variation at very low and very high organic conditions. Differences were larger with methanol compared with acetonitrile containing solvent compositions and when applied without a column or with very long connecting tubing.

I thank Janssen Pharmaceutica and especially Dr Filip Cuyckens for the internship position for letting to gain experience in an industry setting and study these effects. Additionally, I thank Erasmus+ mobility and Smart specialization doctoral stipend for funding my stay.

Group seminar at Pühajärve

Ernesto giving his talk

From 24th to 25th of November our group had a traditional biannual seminar in Pühajärve Spa hotel. The seminar is a nice opportunity to learn about what the group members are doing and which challenges they are tackling. The presentations covered a broad domain of analytical chemistry from fundamental acid-base studies to bioanalyses and analyses of cultural heritage.

Ambient ionization and fluoroalcohols to improve bioanalysis

The first session was focusing on the bioanalytics. Max, a PhD fellow doing an internship in London right now, presented the results of drug analyses from a music festival. Next to strongly varying drug dose, the problem is the strongly varying dissolution of corresponding dose. Next two presentations presented by Rūta, a PhD fellow, and Krit, her undergraduate student introduced fluoroalcohols as novel LC eluent additives and their effect on retention mechanism and electrospray sensitivity. It was really interesting how strongly and unexpectedly differently some fluoroalcohols may change the retention mechanism.

The reliability of fluorescence measurement

The second session focused on acid-base and coordination chemistry. Alo, a PhD fellow, presented his improvements and challenges in the synthesis of bambusuril derivatives. Elisabeth, a master student, introduced 19F NMR measurements of pKa of fluorinated compounds in acetonitrile. Sigrid, a PhD fellow, gave a lecture on how to measure correct fluorescence spectra accounting all effects that may affect the spectra. She showed the importance of concentration and the inner filter effects correction on fluorescence spectrum. Andre, a PhD fellow, wrapped up the seminar with the presentation of his results in gas phase acidity measurements.

Did I get real cashmere scarf from the market?

The third session was focusing on the analysis of cultural heritage. Eliise, a PhD fellow, presented the comparison of four most applied derivatization procedures for analysis of binders in GC. Pilleriin, a PhD fellow, presented her results of textile analyses and a model developed  to classify unknown textiles using ATR-FT-IR spectroscopy. Markus, a master student, presented his work on coupling LC with nano-ESI FT-ICR-MS. Juhan, an undergraduate student, introduced his work on acid-base measurements of fluorophoric pH sensor molecules.

After inspiring presentation and fruitful discussions, we had a nice opportunity to relax in the spa and sauna. Additionally, group members discussed with Prof. Leito and Associate Prof. Herodes the SR-15 report from IPCC.

Is open science in terms of metadata really possible?

Next day was kicked off by Astrid, a PhD fellow, who compared the measurement of binding constants using isothermal calorimetry and NMR. Next, Piia, a PhD fellow, introduced her results on using the data from the literature to test, validate and improve the electrospray ionization efficiency prediction model. The take-home message from Piia’s presentation was the need for data integrity on results one is reporting and clear explanations on how one obtained these results. Additionally, a machine-readable format of the structure is a great help to simplify data mining from literature. Next, Jaanus, a PhD fellow introduced the results from a collaboration with a visiting PhD fellow Tingting Wang from DTU, Denmark. He showed the results of standard substance free quantification in the example of pesticides in food matrices. Ernesto, a PhD fellow, introduced his doctoral project on designing and describing the anionic derivatization reagents in LC/MS.

What’s causing this smell?

The second day was wrapped up by Associate Prof. Koit Herodes. He showed us a case study on the analysis of smell of ruined goods. Finally, he presented the current edition of validation software our group is developing to simplify and automate the validation in LC/MS analyses.

Thanks to all participants for interesting and inspiring presentation and for fruitful discussions.

MSACL EU 5th Annual Congress & Exhibits in Salzburg

From the 9th to the 13th of September MSACL EU 2018 Annual Congress took place in the cosy city of Salzburg, Austria. This conference was designed to mass spectrometry audience mainly focusing on clinical applications.  I had the opportunity to participate in this inspiring conference. Moreover, I had the possibility to give a talk. I introduced our studies on standard substance free quantitation in LC/ESI/MS analysis.

Lightning talks to encourage young scientists

Prof. Jerzy Adamski kicked off the conference with the plenary lecture on the topic “Metabolomics Messages on Human Health and Diseases”. As one of the main goals of this conference is to inspire and encourage the young scientists the next session was lightning talks. Poster presenters had 90 seconds and one slide to present their research and cultivate interest in their topic. Additional possibility to get to know mature scientist was the program “meet the experts”. There were short meetings as well as booth and poster tours with experts. I had the possibility to analyze some posters together with Dr. Oleg Mayboroda from Leiden University Medical Centre. It was nice to see how the experts look at the posters and how and which questions they ask. Dr. Mayboroda gave a checklist of how to assess the goodness of the PCA plot presented on posters.

Scientific highlights of the conference

There were 5 parallel sessions every day. For me, the three highlights were as follows.  First of all, Dr. Mario Thevis gave a talk about mass spectrometry in sports drug testing. Also, Prof. David Millington gave an interesting talk about the role of tandem mass spectrometry in newborn screening. It was encouraging to see how the methods developed by his team save around 2500 newborns on yearly basis. Furthermore, Dr. Lyudmilla Yanshole gave a talk about using postmortem tissues for biomarker identification. It is an interesting study as for lots of diseases it is very difficult to get tissue of healthy species.

Standard substance free quantification LC/ESI/MS

I had the possibility to present for the first time a talk at an international conference. For that, I am most grateful for the MSACL organization and the scientific committee. I introduced the recent results on the feasibility of standard substance free (semi)quantitation in LC/ESI/MS using ionization efficiency prediction models. We have measured more than 2000 ionization efficiency values. We have incorporated 21 solvent compositions. The models are developed based on descriptors calculated from the 2D structure of compounds and the predictions perform well even in complex matrices, namely, bodily fluids. Our average misprediction of ionization efficiencies is less than 3.5 times mismatch.  I thank the audience for fruitful discussions on the topic.

Salzburg is a lovely city with stunning views of the Alps. Furthermore, the organizer made our stay at the conference very enjoyable with the nice coffee breaks and warm buffet for lunch and dinner which were offered every day.


Is it possible to use data below the limit of quantitation in pharmacokinetic studies?

Results below the limit of quantification (BLQ) are generally not reported or reported without explicit numbers, leaving pharmacokinetic (PK) and pharmacodynamic (PD) studies wishing for more information to improve their model parameters. But the laboratory cannot release actual values BLQ since the quality of that data has never been assessed.

Possible solutions to this unfortunate situation were investigated in a recent perspective article led by our group and published in Bioanalysis. The article titled: “Utilization of data below the analytical limit of quantitation in pharmacokinetic analysis and modelling: promoting interdisciplinary debate”, expanse the so far used statistical salvage of information, by an experimental addition to investigate the quality of data BLQ.

By directing this article towards the pharmacometrician, the analytical scientist and the regulatory personnel, we hope to encourage an inter-disciplinary discussion to improve the situation by finding ways to use BLQ data in PK/PD studies, in order to enhance the quality of the obtained pharmacokinetic models. Several ways were proposed for moving forward, in particular improving/modifying method validation guidelines for enabling to use BLQ data and leaving the decision regarding whether and how to incorporate the BLQ data into a PK/PD model to the data analyst and not the analytical chemist.

ASMS 2018 in San Diego

Piia Liigand giving her talk

On 3rd-7th June three members of our group focusing on ionization efficiency studies Dr. Anneli Kruve-Viil, PhD students Piia Liigand and Jaanus Liigand, participated in the 66th Annual Conference of American Society for Mass Spectrometry (ASMS) in San Diego, CA. The conference was a huge success. There were altogether about 7500 scientists participating, ca 200 oral presentations and 3300 of posters. We had two oral presentations and one poster presentation.

The conference was kicked off by a presentation by Lisa Shipley from Merck who gave a very informative talk about smart trials and moving to patient-centric clinical trials – most probably the future of clinical trials. It was very inspiring to see how a field that is considered to be relatively conservative is picking up the most modern technical solutions such as clever packages and home-based sample collection.

The first full day of the conference started with a presentation by our PhD student Piia, who gave a talk about achieving more accurate semi-quantitative analysis by predicting electrospray ionization efficiencies. She first gave an overview of the research carried out so far and then, introduced her latest results. She showed that with the help of using ionization efficiencies, concentration estimation in various biological matrices was improved by more than an order of magnitude.

Jaanus Liigand presenting his poster

Jaanus presented a poster on semiquantitative LC/ESI/MS via ionization efficiency prediction. He presented the simple and user-friendly approach of predicting ionization efficiencies using only 2D structures. We are now able to predict ionization efficiencies in both ESI positive and negative mode and in different solvent compositions without time-consuming DFT-COSMO calculations. Additionally, we have shown that using ionization efficiency predictions the validation with LC gradient elution resulted in 2.7-fold mispredicted concentrations compared to 44-fold mispredictions using directly peak areas. We were happy to see that numerous groups were interested in our studies and fruitful discussions about the results did not stop until the end of the poster session.

Dr. Anneli Kruve-Viil giving her talk

Dr. Anneli Kruve-Viil presented some of the latest results obtained in FU Berlin. She talked about using mass spectrometry and ion mobility spectrometry for investigating interlocked nature of catenanes and knots. These results will soon be shared with everyone.

In conclusion, this year’s ASMS was very successful for our group. We saw a lot of interest in our work, met our collaborators and got some new friends and possible future collaborators. We are already looking forward to the next ASMS in Atlanta. We are also grateful for our financial supporters, who made this conference possible to us: instrumentation provided by Estonian Center of Analytical Chemistry (, Ministry of Education and Research of Estonia by smart specialization doctoral stipend, Graduate School of Functional Materials and Technologies, and Alexander von Humboldt Foundation.

More information about the group focusing on ionization efficiency studies can be found on the webpage

Another motivational group seminar took place on last weekend, 5-6th May

Traditional analytical chemistry group seminar was this time held in beautiful Voore Guest House on 5-6th of May. Despite the sunny and wonderful weather outside, a group of analytical chemists were pleased to stay inside to discuss research. Since many of our group members are going to defend their theses soon (PhD students Märt Lõkov and Sofja Tšepelevitš, master’s students Alo Rüütel and Andre Leesment, and bachelor’s students Elisabeth Parman and Lisett Kiudorv), their presentations were followed by many questions and fruitful discussions. Another PhD student, Max Hecht, joined us via Skype and gave us an interesting presentation about sponge spray while reminding that every chemist must face many problems and difficulties before gaining the expected results. Besides numerous analytical chemistry research-related presentations, our research fellow Dr. Riin Rebane, who is currently studying law, introduced us a world of law and talked about patent applications in Estonia. The whole seminar was finished with a gripping presentation about postdoctoral studies in the University of Helsinki by Dr. Hanno Evard.
In addition to the intense seminar, we were able to enjoy the beautiful nature and landscape of Vooremaa while taking a long walk in the village and discussing the day’s events in a hot sauna.

Recent study emphasizes that pesticide traces in Estonian groundwater under farmlands exceed the allowed limit

Sum of pesticide traces in samples from 2016-2017. Source: Estonian Environmental Research Centre

Our joint research fellow with Estonian Environmental Research Centre Dr. Riin Rebane and joint PhD candidate Siiri Saaver participated in the study “Analysis of pesticide traces and dynamics in surface and groundwater” . In this study, 137 surface and groundwater samples from all over Estonia were analysed with a targeted screening of 135 pesticides. From 137 analysed samples 49 pesticide traces were detected in more than half of the samples. In 34 samples 9 pesticides and their metabolites exceeded the allowed concentration level of 0.1 μg/L. In 9 samples pesticides and their transformation products exceeded 0.5 μg/L. Interestingly, the main compound found (in 26 samples) was chloridazon-desphenyl, which is a metabolite of pesticide chloridazon that is not registered on Estonian market and therefore not sold, which makes the determination of the origin of this compound complicated. It needs further research whether it is a remnant of Soviet times and slowly moving in the soil towards groundwater or if it is in use now.
This study was also reported in news portal Novaator and in environmental TV show Osoon

Moreover, there are hundreds of different pesticides and targeted screening methods usually look for compounds that are banned or known to be problematic. This study used the broader list of pesticides than regular yearly monitoring of pesticides indicating that broader coverage of potential pollutants is needed. Therefore, there is a need for the suspect and non-target screening methods for detecting more compounds and their metabolites.

In collaboration with Estonian Environmental Research Centre, our group has also contributed to studying and developing the non-target approach. Namely, Gunnar Printsmann developed in his master thesis suspect and non-target screening method for groundwater using high-resolution mass spectrometry which also included pollutants database. He found and confirmed a new industrial pollutant dibutyl phthalate in one sample from North-Eastern Estonia.

Belgian Society for Mass Spectrometry 2018 Annual Meeting

Our PhD student Jaanus is currently doing research in the group of Prof. Edwin De Pauw at the University of Liege in Belgium and he had a nice opportunity to take part in a 21st annual meeting of Belgian Society for Mass Spectrometry that was held on 29th of March in Liege. The meeting was organized in honour of Prof. Edwin De Pauw to summarize his work as he intended to retire after this year. Luckily for the mass spectrometric community, he will be actively involved in the research at least for four coming years.

Prof. Scott McLuckey opened the day with a presentation about strategies for achieving enzyme-like specificity in the gas-phase fragmentation of peptide and proteins. He showed different strategies how to cleave for example specifically at asparagine or lysine.

Prof. Andrea Sinz presented the results of the development of cleavable cross-linkers. Additionally, she pointed out that although cleavable crosslinkers are available on the market most of the groups determining the protein structures still use the noncleavable crosslinkers and do not take advantage of additional information provided by cleavable crosslinkers.

Dr. Valérie Gabelica presented the results of the studies of nucleic acid noncovalent complexes in native MS. She said that by knowing and studying the fundamentals of ESI processes one gets also a real insight into phenomena seen in different applications (in her case, nucleic acid noncovalent complexes). She also pointed out that unfortunately, scientific community publishes solely positive results which result in biased and non-universal theories.

Jaanus Liigand also had the possibility to present the results of our studies of standard substance free quantitation in LC/ESI/MS analysis and industry showed a great interest in our approach which could be beneficial for their needs (see the poster here).

It was a really nice day full of interesting presentations and discussions.

European Mass Spectrometry Conference 2018

Dr. Anneli Kruve giving her talk at EMSC 2018
Dr. Anneli Kruve giving her talk at EMSC 2018

Dr. Anneli Kruve, a leader of research team focussing on ionization efficiency studies in electrospray, is currently a Humboldt fellow in Freie Universität Berlin and visited the 1st European Mass Spectrometry Conference in Saarbrücken (Germany) this month. She describes some of the highlights of this conference in her blog, you can read the post below.


Last week I had a chance to take part in the European Mass Spectrometry Conference that was hosted by DGMS (German Society for Mass Spectrometry) and SFSM (French Society for Mass Spectrometry). Below I share a few key ideas from this nice conference that took place in Saarbrücken over 5 days.

The conference was opened with a plenary lecture by Prof. Alain van Dorsselaer who summarized the main work he and his group has done on mass spec during the last 30 years. One of the key ideas, that came up several times in his talk referred to the fact that endless possibilities are accompanied by extreme data load. The amount of data in LC/MS/MS is huge and it is very complicated to analyse these massive data sets. Several other scientists, including Prof. Andreas Roempp and his group, also stressed the importance of transparent and open source data analyses and storage that could eventually simplify the data treatment. These ideas strongly resonate with my own ideas of applying more data science tools in primary data treatment in mass spectrometry, as today the data processing is by far limiting the progress in several fields of analytical mass spectrometry. Mostly this is the case for fields, where the science is still in the “discovery” stage; meaning that the scientists aim at finding the important compounds and yet do not know which these compounds could be. Such fields include metabolomics, proteomics, environmental science, etc.

Prof. Philippe Schmitt Kopplin stressed the importance of high throughput in metabolic sample analyses and explained why dissolve-and-shoot approach (flow-injection or infusion combined with MS) is often most practical. Also, he showed several case studies where marker compounds could be reliably identified with this simple approach if accompanied with efficient and accurate data processing. A particularly interesting example was a case study of 170-year-old wine from the bottom of the Baltic Sea.

Prof. Carsten Engelhard showed an extremely clever, almost brilliant, method to analyse nanoparticles with simple dilution & infusion experiment. The infusion of homogeneous solution to ICP-MS instrument causes an almost constant signal with small random variations. However, if the solution of nanoparticles is infused to ICP-MS, most of the time there is no signal (only noise). When one of the nanoparticles enters the plasma a signal suddenly occurs causing a peak in the chronogram. The height of the signal reflects the size of the nanoparticle and the number of peaks per volume indicates the concentration of the nanoparticles.

Prof. Thomas Kraemer introduced us to the world of forensic analyses. Particularly, he focused on MALDI imaging techniques, that allow revealing drug intake or exposure to toxic compounds. For this purpose his lab is using two types of samples, the traditional hair and lately also toenails, to overcome the problem arising for hairless people. Interestingly, the single hair analysis also reveals time-resolved information with high precision; therefore, allowing to distinguish between one-time and long time exposures.

You can check out more posts from our team studying ionization efficiencies