<p><strong>For the first time, thorium nuclei have now been successfully transferred from one state to another using a laser – but there has already been speculation for decades about the technical possibilities that would arise if this feat were one day possible. Expectations are high: probably the best-known idea is the nuclear clock, but precision measurements based on the thorium transition could open up new possibilities in completely different areas of research.</strong></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/TU_Wien_Nuclear_Clocks_and_the_Fundamental_Constants_of_Nature_The_nuclear_clock_a_spectacular_application_made_possible_by_the_discovery_of_the_thorium_transition_cbfb93c6fb.jpg" alt="TU Wien: The nuclear clock: a spectacular application, made possible by the discovery of the thorium transition."/></p>
<h4><strong>Time measurement</strong></h4>
<p>The most accurate time measuring devices today are atomic clocks – they have even changed the definition of our units of time. Today, the second is defined as the length of time corresponding to a very specific number of oscillations of the light that must be shone on a caesium atom in order to switch its electrons from one state to another.</p>
<p>Similar to the pendulum of a pendulum clock, the light oscillation of the caesium atoms plays the role of the timer that provides the regular ticking for the most accurate time measurement possible. Today, atomic clocks are used, for example, for the coordination of satellites, they enable the high accuracy of GPS signals and they also play a role in telecommunications.</p>
<p>Instead of cesium atoms, however, thorium atomic nuclei can now also be used for keeping time. Only when the thorium nuclei are irradiated with a laser beam of exactly the right frequency do they change their state. If the laser changes its frequency slightly (e.g. due to external interference), this immediately results in a change of the response of the thorium nuclei. The combination of laser and thorium nuclei therefore makes it possible to keep the laser frequency extremely stable and ensures that the laser frequency does not drift away.</p>
<p>Because atomic nuclei are much smaller than atoms and much less sensitive to electromagnetic perturbations, atomic nuclei can achieve much higher precision than atoms when it comes to measuring time.</p>
<h4><strong>Everything gets better with better clocks</strong></h4>
<p>With better time measurement, other physical quantities can also be measured more accurately. This is a well-known phenomenon: in nautical navigation, for example, people have struggled for a long time with the problem that although it is easy to determine the latitude based on the position of the sun, an accurate clock is required to calculate the longitude correctly. Better time measurement often makes other measurements possible.</p>
<p>For example, Einstein&#39;s theory of relativity states that time does not pass in the same way everywhere: the flow of time depends on the gravitational field. In this way, an extremely precise clock could therefore be used to accurately measure the Earth&#39;s gravitational field – with many possible applications ranging from the search for mineral resources to research into plate tectonics and earthquake prediction.</p>
<p>Great hopes are also pinned on the possibility that new, better clocks could clarify previously unsolved fundamental questions of physics: If it is possible to measure the constants of nature much more accurately than before, then it would also be possible to test the theory that these natural constants may not be perfectly constant at all. Perhaps they change over time? Research into dark matter is also hoping to gain new insights through even more precise measurements.</p>
<p>It is not always possible to get closer to the fundamental laws of nature just by looking at the smallest particles in a particle accelerator or by looking at the most distant regions of space. Sometimes you just need greater precision – and this is where the newly discovered thorium transition and all its potential applications should help in the coming years and decades.</p>
<h4><strong>Back to the main article:</strong></h4>
<ul>
<li><a href="https://gcms.labrulez.com/article/4273"><strong>Atomic Nucleus Excited with Laser: A Breakthrough after Decades</strong></a></li>
</ul>


Nuclear Clocks and the Fundamental Constants of Nature

<p><strong>Physicists have been hoping for this moment for a long time: for many years, scientists all around the world have been searching for a very specific state of thorium atomic nuclei that promises revolutionary technological applications. It could be used, for example, to build an nuclear clock that could measure time more precisely than the best atomic clocks available today. It could also be used to answer completely new fundamental questions in physics - for example, the question of whether the constants of nature are actually constant or whether they change in space and time.</strong></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/TU_Wien_Oliver_Diekmann_Atomic_Nucleus_Excited_with_Laser_A_Breakthrough_after_Decades_A_laser_beam_changes_the_state_of_thorium_nucleui_which_are_embedded_in_a_crystal_940b6404dc.jpg" alt="TU Wien / Oliver Diekmann: A laser beam changes the state of thorium nuclei, which are embedded in a crystal."/></p>
<p>Now this hope has come true: the long-sought thorium transition has been found, its energy is now known exactly. For the first time, it has been possible to use a laser to transfer an atomic nucleus into a state of higher energy and then precisely track its return to its original state. This makes it possible to combine two areas of physics that previously had little to do with each other: classical quantum physics and nuclear physics. A crucial prerequisite for this success was the development of special thorium-containing crystals. A research team led by Prof. Thorsten Schumm from TU Wien (Vienna) has now published this success together with a team from the National Metrology Institute Braunschweig (PTB) in the journal &quot;Physical Review Letters&quot;.</p>
<blockquote>
<p><strong>The &quot;thorium transition&quot;, which physicists have been looking for for decades, has now been excited for the first time with lasers. This paves the way for revolutionary high precision technologies, including nuclear clocks.</strong></p>
</blockquote>
<h4><strong>Switching quantum states</strong></h4>
<p>Manipulating atoms or molecules with lasers is commonplace today: if the wavelength of the laser is chosen exactly right, atoms or molecules can be switched from one state to another. In this way, the energies of atoms or molecules can be measured very precisely. Many precision measurement techniques are based on this, such as today&#39;s atomic clocks, but also chemical analysis methods. Lasers are also often used in quantum computers to store information in atoms or molecules.</p>
<p>For a long time, however, it seemed impossible to apply these techniques to atomic nuclei. <em>&quot;Atomic nuclei can also switch between different quantum states. However, it usually takes much more energy to change an atomic nucleus from one state to another – at least a thousand times the energy of electrons in an atom or a molecule,&quot;</em> says Thorsten Schumm. <em>&quot;This is why normally atomic nuclei cannot be manipulated with lasers. The energy of the photons is simply not enough.&quot;</em></p>
<p>This is unfortunate, because atomic nuclei are actually the perfect quantum objects for precision measurements: They are much smaller than atoms and molecules and are therefore much less susceptible to external disturbances, such as electromagnetic fields. In principle, they would therefore allow measurements with unprecedented accuracy.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/TU_Wien_Foto_Wilke_Atomic_Nucleus_Excited_with_Laser_A_Breakthrough_after_Decades_Thorsten_Schumm_with_a_crystal_containing_thorium_03f3d62c0f.jpg" alt="TU Wien / Foto Wilke: Thorsten Schumm with a crystal containing thorium."/></p>
<h4><strong>The needle in the haystack</strong></h4>
<p>Since the 1970s, there has been speculation that there might be a special atomic nucleus which, unlike other nuclei, could perhaps be manipulated with a laser, namely thorium-229. This nucleus has two very closely adjacent energy states – so closely adjacent that a laser should in principle be sufficient to change the state of the atomic nucleus.</p>
<p>For a long time, however, there was only indirect evidence of the existence of this transition. <em>&quot;The problem is that you have to know the energy of the transition extremely precisely in order to be able to induce the transition with a laser beam,&quot;</em> says Thorsten Schumm. <em>&quot;Knowing the energy of this transition to within one electron volt is of little use, if you have to hit the right energy with a precision of one millionth of an electron volt in order to detect the transition.”</em> It is like looking for a needle in a haystack – or trying to find a small treasure chest buried on a kilometer-long island.</p>
<h4><strong>The thorium crystal trick</strong></h4>
<p>Some research groups have tried to study thorium nuclei by holding them individually in place in electromagnetic traps. However, Thorsten Schumm and his team chose a completely different technique. <em>&quot;We developed crystals in which large numbers of thorium atoms are incorporated,&quot;</em> explains Fabian Schaden, who developed the crystals in Vienna and measured them together with the PTB team. <em>&quot;Although this is technically quite complex, it has the advantage that we can not only study individual thorium nuclei in this way but can hit approximately ten to the power of seventeen thorium nuclei simultaneously with the laser – about a million times more than there are stars in our galaxy.&quot;</em> The large number of thorium nuclei amplifies the effect, shortens the required measurement time and increases the probability of actually finding the energy transition.</p>
<p>On November 21, 2023, the team was finally successful: the correct energy of the thorium transition was hit exactly, the thorium nuclei delivered a clear signal for the first time. The laser beam had actually switched their state. After careful examination and evaluation of the data, the result has now been published.</p>
<p><em>&quot;For us, this is a dream coming true,&quot;</em> says Thorsten Schumm. Since 2009, Schumm had focused his research entirely on the search for the thorium transition. His group as well as competing teams from all over the world have repeatedly achieved important partial successes in recent years. <em>&quot;Of course we are delighted that we are now the ones who can present the crucial breakthrough: The first targeted laser excitation of an atomic nucleus,&quot;</em> says Schumm.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/TU_Wien_PTB_Atomic_Nucleus_Excited_with_Laser_A_Breakthrough_after_Decades_PTB_researcher_Johannes_Tiedau_in_the_laser_lab_e7fa06332a.jpg" alt="TU Wien / PTB: PTB-researcher Johannes Tiedau in the laser lab."/></p>
<h4><strong>The dream of the atomic nucleus clock</strong></h4>
<p>This marks the start of a new exciting era of research: now that the team knows how to excite the thorium state, this technology can be used for precision measurements. <em>&quot;From the very beginning, building an atomic clock was an important long-term goal,&quot;</em> says Thorsten Schumm. <em>&quot;Similar to how a pendulum clock uses the swinging of the pendulum as a timer, the oscillation of the light that excites the thorium transition could be used as a timer for a new type of clock that would be significantly more accurate than the best atomic clocks available today.&quot;</em></p>
<p>But it is not just time that could be measured much more precisely in this way than before. For example, the Earth&#39;s gravitational field could be analyzed so precisely that it could provide indications of mineral resources or earthquakes. The measurement method could also be used to get to the bottom of fundamental mysteries of physics: Are the constants of nature really constant? Or can tiny changes perhaps be measured over time? <em>&quot;Our measuring method is just the beginning,&quot;</em> says Thorsten Schumm. <em>&quot;We cannot yet predict what results we will achieve with it. It will certainly be very exciting.&quot;</em></p>


Atomic Nucleus Excited with Laser: A Breakthrough after Decades

<p><strong>Vaping aerosols contain thousands of unknown chemicals and substances not disclosed by manufacturers, including industrial chemicals and caffeine, Johns Hopkins University researchers found.</strong></p>
<p><strong>The study is the first to apply to vaping liquids and aerosols an advanced fingerprinting technique used to identify chemicals in food and wastewater. The results, <a href="https://pubs.acs.org/doi/10.1021/acs.chemrestox.1c00253">just published in the journal <em>Chemical Research in Toxicology</em></a>, suggest people who vape are using a product whose risks have yet to be fully determined and could be exposing themselves to chemicals with adverse health effects.</strong></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Johns_Hopkins_University_WILL_KIRK_JOHNS_HOPKINS_RESEARCHERS_FIND_THOUSANDS_OF_UNKNOWN_CHEMICALS_IN_ELECTRONIC_CIGARETTES_9b00c7b9b3.jpg" alt="Johns Hopkins University / Will Kirk: Johns Hopkins Researchers Find Thousands of Unknown Chemicals in Electronic Cigarettes."/></p>
<p><em>&quot;Existing research that compared e-cigarettes with normal cigarettes found that cigarette contaminants are much lower in e-cigarettes. The problem is that e-cigarette aerosols contain other completely uncharacterized chemicals that might have health risks that we don&#39;t yet know about,&quot;</em> said senior author <a href="https://engineering.jhu.edu/ehe/faculty/carsten-prasse/"><strong>Carsten Prasse</strong></a>, an assistant professor of environmental health and engineering at the <a href="https://engineering.jhu.edu/"><strong>Whiting School of Engineering</strong></a> and the <a href="https://publichealth.jhu.edu/"><strong>Bloomberg School of Public Health</strong></a>. <em>&quot;More and more young people are using these e-cigarettes and they need to know what they&#39;re being exposed to.&quot;</em></p>
<p>Previous studies of e-cigarettes have looked specifically for evidence of the hazardous chemicals found in traditional cigarettes. But here the researchers performed a nontargeted analysis to explore the full range of chemicals both in the vaping liquid and the aerosols.</p>
<p>Prasse and his team were the first researchers to test vape samples with chromatography/high-resolution mass spectrometry, a chemical fingerprinting technique more commonly used to identify organic compounds in wastewater, food, and blood. Although it&#39;s possible to buy vaping products in hundreds of flavors, for consistency they tested only tobacco-flavored liquids sold by four popular brands—Mi-Salt, Vuse, Juul, and Blu. They found thousands of unknown chemicals in the liquid, and the number of compounds increased significantly in the aerosol. Furthermore, they detected condensed hydrocarbon-like compounds, typically associated with combustion, which manufacturers say is not happening during vaping. In traditional cigarettes, the condensed hydrocarbons generated during combustion are toxic.</p>
<blockquote>
<h4>&quot;I HAVE A PROBLEM WITH HOW VAPING IS BEING MARKETED AS MORE HEALTHY THAN SMOKING CIGARETTES. IN MY OPINION WE ARE JUST NOT AT THE POINT WHEN WE CAN REALLY SAY THAT.&quot;</h4>
</blockquote>
<blockquote>
<p>Carsten Prasse</p>
<h6>Assistant professor, School of Engineering</h6>
</blockquote>
<p><em>&quot;One of the main ways electronic cigarettes have been marketed is that they operate at temperatures below combustion, which would make them safer than traditional smoking,&quot;</em> said lead author Mina Tehrani, a postdoctoral fellow in the School of Public Health. <em>&quot;Our study shows that this novel fingerprinting approach can be applied to assess whether combustion-like processes are going on.&quot;</em></p>
<p>The team found nearly 2,000 chemicals, the vast majority of which are unidentified. Of those the team could identify, six substances were potentially harmful, including three chemicals never previously found in e-cigarettes. Tehrani was particularly surprised to find the stimulant caffeine in two of the four products. Caffeine has previously been detected in e-cigarettes but only in the caffeine-oriented flavors like coffee and chocolate.</p>
<p><em>&quot;That might be giving smokers an extra kick that is not disclosed,&quot;</em> she said. <em>&quot;We wonder if they are adding it intentionally.&quot;</em></p>
<p>Besides caffeine, the team found three industrial chemicals, a pesticide, and two flavorings linked with possible toxic effects and respiratory irritation.</p>
<p>Prasse said he became interested in studying vaping products after his cousin, a former smoker, started vaping, insisting it was healthy. He plans to send that cousin this paper.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Johns_Hopkins_University_WILL_KIRK_JOHNS_HOPKINS_RESEARCHERS_FIND_THOUSANDS_OF_UNKNOWN_CHEMICALS_IN_ELECTRONIC_CIGARETTES_1_f38915afda.jpg" alt="Johns Hopkins University / Will Kirk: Johns Hopkins Researchers Find Thousands of Unknown Chemicals in Electronic Cigarettes."/></p>
<p><em>&quot;People just need to know that they&#39;re inhaling a very complex mixture of chemicals when they vape. And for a lot of these compounds we have no idea what they actually are,&quot;</em> Prasse said. <em>&quot;I have a problem with how vaping is being marketed as more healthy than smoking cigarettes. In my opinion we are just not at the point when we can really say that.&quot;</em></p>
<p>Co-author Ana M. Rule, an expert in metals exposures from vaping with the Johns Hopkins Bloomberg School of Public Health, says many young people who vape never smoked—so they aren&#39;t making a healthier choice, only starting out with a risky one.</p>
<p><em>&quot;There are millions of middle school and high school students vaping that would not otherwise think of smoking,&quot;</em> she says. <em>&quot;For them there is no risk reduction, only increased risk.&quot;</em></p>
<p>Authors also include Matthew N. Newmeyer, a postdoctoral fellow at the Johns Hopkins Bloomberg School of Public Health. The work was supported by grants from the National Institute of Environmental Health Sciences, the National Center for Advancing Translational Sciences, and NIH Roadmap for Medical Research.</p>


Johns Hopkins Researchers Find Thousands of Unknown Chemicals in Electronic Cigarettes

<p><strong>Our Library never stops expanding. What are the most recent contributions to LabRulezLCMS Library in the week of 22th July 2024? Check out new documents from the field of liquid phase, especially HPLC and LC/MS techniques!</strong></p>
<blockquote>
<h4>👉 <a href="https://lcms.labrulez.com/library"><strong>SEARCH THE LARGEST REPOSITORY OF DOCUMENTS ABOUT LCMS AND RELATED TECHNIQUES</strong></a></h4>
</blockquote>
<blockquote>
<p><strong>👉 Need info about different analytical techniques?</strong> Peek into <a href="https://gcms.labrulez.com/library"><strong>LabRulezGCMS</strong></a> or <a href="https://icpms.labrulez.com/library"><strong>LabRulezICPMS</strong></a> libraries.</p>
</blockquote>
<p>This week we bring to you poster presentations from <a href="https://lcms.labrulez.com/events/568"><strong>ASMS 2024</strong></a> by <strong>Agilent Technologies</strong>, <strong>Shimadzu</strong>, <strong>Thermo Fisher Scientific</strong>, and <strong>Waters Corporation</strong>!</p>
<blockquote>
<p>💡 <strong>Almost 1000 ASMS posters and presentations <a href="https://lcms.labrulez.com/library?mainauthorItems=284">available in the LabRulezLCMS library</a></strong> (unique search and filtering)</p>
</blockquote>
<h4><strong>1. Waters Corporation: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/2023_asms_king_liver_178c54e990.pdf">HIGH THROUGHPUT PLASMA PROFILING OF HUMAN LIVER DISEASE SAMPLES USING RAPID CHROMATOGRAPHY AND A MULTI- REFLECTING TIME-OF-FLIGHT MASS SPECTROMETER</a></strong></h4>
<ul>
<li>poster - ASMS 2024</li>
</ul>
<p><strong>Introduction:</strong> Metabolomics is a valuable research strategy in the determination  FIG. 5  FIG. 1  FIG. 7  FIG. 3  of disease progression, disease stratification, the identification of  biological markers for early diagnosis and for the development of  new therapeutics. Acute-on-chronic liver failure (ACLF) is a  condition characterized by systemic inflammation, multiple organ  failure, and high short-term mortality1. ACLF develops from the  acute decompensation of cirrhosis and currently there is no  biomarker identified for the early diagnosis of this disease.  Therefore, fully understanding the role metabolites and lipids play  in the progression of ACLF and its underlining mechanisms could  greatly help determine new diagnostic markers driving  development of new therapeutics. Investigating biomarkers for  large scale studies requires robust, high-throughput analytical  methods.</p>
<p>Rapid microbore metabolic profiling (RAMMP) methods and  conventional high-resolution mass spectrometry have previously  been shown to considerably reduce analysis time2-3. Here we  compare these methods with a vacuum jacketed column  technology (VJC)4-5 and ultra high-resolution mass spectrometry6  for the analysis of plasma from liver disease patients by reversed-  phase (RP) for lipid and hydrophilic interaction chromatography  (HILIC) for small molecules.</p>
<p><strong>Conclusion:</strong></p>
<ul>
<li>Conventional LC-MS methods used for large cohort studies suffer from batch response variation.  The rapid chromatographic methods reduce this impact and demonstrated reproducible response  across the entire batch of 168 injections per polarity (Fig. 2).</li>
<li>The SELECT SERIES MRT mass spectrometer generated highly accurate mass measurements  (&lt;1 ppm), improving annotation confidence for both lipids and small molecules, including essential  amino acids and carnitines from the HILIC analysis (Fig. 3).</li>
<li>PCA of the RAMMP data showed good analytical reproducibility from the clustered QC samples and  group separation with some overlap between the different disease groups (Fig. 4).</li>
<li>Group comparisons were performed by OPLS-DA where statistically significant features were  highlighted for database annotation (Fig. 5).</li>
<li>A number of lipids classes, particularly lysophosphatidylcholines (LPC), phosphatidylcholines (PC)  and sphingomyelins (SM), showed dysregulation in the diseased samples when compared to healthy  controls and were annotated through Lipostar2 with mass accuracies between 0.1-0.3 ppm (Fig. 6).</li>
<li>For the HILIC small molecule analysis, differences in amino acid response were detected in  comparisons between diseased and healthy controls.</li>
<li>The SELECT SERIES MRT MS achieved mass resolution of 170-200K FWHM at 30 Hz compatible with  RAMMP (a) and VJC (b) methodologies for example lipids, PC36:1 (0.18 ppm) and SM42:3, O2 (0.16  ppm), with the VJC providing better peak shape and resolution of adjacent peaks (Fig. 7)</li>
<li>Comparison of the RAMMP and VJC negative lipid analysis showed very similar distribution of  disease and healthy control groups demonstrating minimal impact on the overall statistics (Fig. 8).</li>
<li>Both RAMMP and VJC methodologies combined with the SELECT SERIES MRT provided highly  accurate reproducible metabolic profiling for a biomarker study, with the VJC providing improved  peak fidelity complemented by the fast scanning high resolution capabilities of the SELECT SERIES  MRT.</li>
<li>This work demonstrated an accurate, reproducible and high throughput metabolomic method for the  rapid screening of a large number of biological samples for biomarker discovery.</li>
</ul>
<h4><strong>2. Thermo Fisher Scientific: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/po_143_characterization_structure_adenopeptin_lc_hram_ms_po143_asms2024_en_7ae893f36c.pdf">In-depth characterization and structure elucidation of non-ribosomal peptides related to adenopeptin using LC-HRAM-MSⁿ</a></strong></h4>
<ul>
<li>Poster - ASMS 2024</li>
</ul>
<h5><strong>Abstract</strong></h5>
<p><strong>Purpose:</strong> Characterization of adenopeptin and related peptaibol analogs in a crude fermentation broth extract using LC-HRAM-MSn to identify adenopeptin congeners and elucidate their structures. Methods: Adenopeptin and its analogs were separated using reversed phase chromatography and analyzed using multi-stage fragmentation on a Thermo Scientific Orbitrap IQ-X Tribrid mass spectrometer. </p>
<p><strong>Results:</strong> Several analogs of adenopeptin differing by one or more methyl groups could be detected and the site of their modification could be narrowed to specific amino acid residues based on their fragmentation patterns.</p>
<h5><strong>Conclusions</strong></h5>
<p>The LC/MS analysis of the crude adenopeptin extract revealed the presence of eight analogs above 0.5% relative MS-abundance, mainly resulting from ”demethylations”, i.e., substitution of Aib for Iva residues. Their modification sites could be determined based on shifts in the fragmentation pattern relative to adenopeptin. Additionally, a potentially crucial substitution of pipecolic acid with proline could be detected and verified based on MS3 spectral evidence for compound 4.</p>
<h4><strong>3. Thermo Fisher Scientific: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/po_146_evaluation_automated_low_flow_lc_ms_setup_po146_asms2024_en_1d935eb142.pdf">Evaluation of an Automated “Quick” Optimization Routine to Streamline Low-Flow LC-MS Setup</a></strong></h4>
<ul>
<li>Poster - ASMS 2024</li>
</ul>
<h5><strong>Abstract</strong></h5>
<p><strong>Purpose:</strong> When setting up low flow LC-MS experiments, a user regularly positions an  emitter at an arbitrary fixed distance from the inlet based on visual alignment. A  prototype ion source featuring an emitter mounted on a 3D motorized stage was used  to evaluate a “quick” optimization strategy used to define the active position for  subsequent LC-MS measurements.</p>
<p><strong>Methods:</strong> The basis of the quick optimization routine was established using m/z- and  position-dependent intensity distributions. The routine was evaluated against two  methods to manually set the emitter position.</p>
<p><strong>Results:</strong> All optimization strategies yielded a statistically equivalent number of protein  and peptide identifications. However, the quick optimization routine yielded superior  peak area reproducibility that translated into significantly better emitter-to-emitter  consistency.</p>
<h4><strong>4. Shimadzu: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/ASMS_poster_PESI_v_DMS_170524_fed75d0c1e.pdf">DPiMS-MS (PESI) combined with vacuum differential mobility spectrometry for rapid forensic analysis.</a></strong></h4>
<ul>
<li>Poster - ASMS 2024</li>
</ul>
<p><strong>Introduction</strong></p>
<ul>
<li>Ambient ionisation (AI) mass spectrometry techniques facilitate rapid turn-around of samples, often in a walk-up format with limited sample preparation, with obvious benefits for forensic applications.</li>
<li>The absence of a chromatographic separation enables sub-minute data acquisition. However, this comes with the cost of greater chance of problems with chemical noise and/or interference between isomeric/isobaric compounds.</li>
<li>One way to remove chemical noise and to separate interfering compounds is to add an ion mobility separation to the method.</li>
<li>Here we implement a novel low pressure differential mobility on a DPiMS-8060 (PESI) system and demonstrate performance for steroids and small molecule drugs in saliva.</li>
</ul>
<p><strong>Conclusion</strong></p>
<ul>
<li>These results demonstrate the potential of vDMS to enhance AIMS by removing chemical noise and separating isobaric species.</li>
<li>DPiMS-vDMS-8060 (PESI) retains the high acquisition speed of PESI while adding an additional dimension of separation.</li>
<li>The additional selectivity may lower the LOQ and reduce false positives.</li>
<li>vDMS-MS methods can be applied in a wide range of complex matrices (e.g. urine, plasma).</li>
</ul>
<h4><strong>5. Shimadzu: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/MP_045_Targeted_quantitative_screening_pesticides_using_high_resolution_DIA_spectral_library_matching_238a221a67.pdf">Targeted quantitative screening pesticides in food matrices using high resolution DIA spectral library matching.</a></strong></h4>
<ul>
<li>Poster - ASMS 2024</li>
</ul>
<p><strong>Overview</strong></p>
<ul>
<li>A single, generic untargeted data independent acquisition (DIA) method was developed for the analysis of extended panels of pesticides in food matrices.</li>
<li>The high-resolution LC-MS/MS method was designed for multi-residue screening and quantitation of pesticides to meet the European Union SANTE 11312/2021 v2 guidelines capable of working with extended target pesticide panels.</li>
<li>The MS and DIA-MS/MS method was applied to quantify a routine panel of pesticides but also included an additional target panel of fungicides for qualitative screening.</li>
</ul>
<p><strong>Conclusions</strong></p>
<ul>
<li>Using a single generic LC-MS and DIA-MS/MS method targeted quantitation using ion ratio confirmation (to meet the EU SANTE guidelines) and extended search capabilities with library identification were supported.</li>
<li>The method results in the quantitation of &gt;250 pesticides at or below the default MRL concentration (10 µg/kg).</li>
</ul>
<h4><strong>6. Shimadzu: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/MP_045_Targeted_quantitative_screening_pesticides_using_high_resolution_DIA_spectral_library_matching_238a221a67.pdf">Identification of positional isomers of linoleic acid containing phospholipids involved in pancreatic ductal adenocarcinoma.</a></strong></h4>
<ul>
<li>Poster - ASMS 2024</li>
</ul>
<p><strong>Overview</strong></p>
<ul>
<li>To enhance lipid identification, Oxygen Attachment Dissociation (OAD) MS/MS has been applied to provide double bond specific dissociation, enabling C=C position assignments.</li>
<li>High resolution OAD MS/MS was applied in positive and negative ion mode to provide further confidence in lipid identification in a pancreatic adenocarcinoma biomarker study</li>
</ul>
<p><strong>Conclusions</strong></p>
<ul>
<li>OAD-MS/MS is a high specificity fragmentation technique to enable C=C positional assignments in lipids. Analysis is easy to perform alongside CID-MS/MS and spectra are easy to interpret.</li>
<li>OAD-MS/MS has been applied to structurally characterize lipids found to be potential markers of PDAC in a previous study using high resolution metabolomics analysis by LC-CID-MS/MS and DPiMSᵗᵐ.</li>
<li>The use of this new technology aims to enhance pancreatic cancer research by providing more comprehensive identification needed to understand the biological roles of the lipids identified as potential markers of PDAC.</li>
</ul>
<h4><strong>7. Agilent Technologies: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/po_2dlc_6545xt_monitoring_oxidation_mabs_asms_2024_wp030_en_agilent_77f2bb18d5.pdf">Monitoring oxidation in recombinant monoclonal antibodies at subunit level through two-dimensional liquid chromatography coupled with mass spectrometry</a></strong></h4>
<ul>
<li>Poster - ASMS 2024</li>
</ul>
<p><strong>Introduction:</strong> Oxidation, induced by reactive oxygen species, is a prevalent chemical modification in monoclonal antibodies (mAbs), affecting amino acid residues such as cysteine (C), methionine (M), tryptophan (W), tyrosine (Y), lysine (K), and others (Gupta et al., 2022). Each residue&#39;s oxidation uniquely influences the protein&#39;s structure and function. Methionine is highly prone to oxidation in mAbs, typically resulting in the formation of a methionine sulfoxide product with increased polarity. These methionine residues are found in both the antigen-binding (Fab) and effector activity (Fc) domains of a mAb, with those situated on the surface being particularly susceptible to oxidation (Hageman et al., 2019). The increasing popularity of two-dimensional liquid chromatography (2D-LC) has led to a significant rise in the integration of two complementary chromatographic techniques, coupled with mass spectrometry (MS), aiming to provide comprehensive insights into mAb post-translational modifications (PTMs) (Sarin et al., 2022). The proposed 2D WCX-RP-MS workflow enables the analysis of mAbs at the subunit level, providing an automated analytical platform for characterizing and identifying oxidized regions within both the Fc and Fab domains.</p>
<p><strong>Conclusions:</strong> The oxidized peaks not resolved by 1D methods are successfully resolved by the D2 RPC column with additional HC-LC information. It should be highlighted that the proposed method completely uses MS compatible buffers and is a faster method to identify mAb modification and their correlation in different mAb fragments compared to the tedious bottomup approach. A general mAb bottom-up analysis takes up to 24-48 hours with the risk of sample loss, degradation, and induced modifications. In the present study, sample preparation took only 4-10 hours (depending on oxidation incubation), and sample analysis took only 3 hours. Hence, 7-13 hours is enough for the subunit analysis with a low risk of sample loss and degradation. The present study focuses on oxidation as the chemical modification of interest, but the workflow can be extended to other critical charge modifications easily resolved by the WCX column.</p>
<h4><strong>8. Agilent Technologies: <a href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/po_2dlc_6545xt_monitoring_oxidation_mabs_asms_2024_wp030_en_agilent_77f2bb18d5.pdf">Flash Characterization of mAbs Using a Combination of Reagents via Automated On-Line Microdroplet Reaction</a></strong></h4>
<ul>
<li>Poster - ASMS 2024</li>
</ul>
<p><strong>Introduction:</strong> Recently, an unmodified Agilent Jet Stream ESI source (AJS) was used to demonstrate “Flash Characterization” of mAbs by microdroplet facilitated reductions or enzyme digestions with good reproducibility and high yield 1. These results motivated us to evaluate treatments that combined enzymatic digestion, reduction, and/or deglycosylation of mAb in a single microdroplet experiment. New optimization parameters for the Agilent Injection Program on Agilent 1290 Infinity II LC were presented. Microdroplet experiments, including GlycINATOR ® deglycosylation, the combination of IdeS cleavage and DTT reduction and IdeS cleavage and GlycINATOR ® deglycosylation were examined for reproducibility, intact mAb remaining after treatments and simplified subunit characterization. GlycINATOR is an endoglycosidase that cleaves N-linked glycans and leaves the core GlcNAc residue with or without a fucose on the asparagine. Additional antibodies of Herceptin and sigmamab are also studied with the combination treatment in the microdroplet reaction.</p>
<p><strong>Conclusions:</strong> </p>
<ul>
<li>Flash Characterization of mAbs with an automatic injector, combination treatments, and microdroplet reaction in the AJS source demonstrates simplification, reproducibility, and cost reduction of protein characterization. </li>
<li>Combination treatments are viable with microdroplet reactions to accelerate the reduction, cleavage, and deglycosylation of native IgG1 significantly.</li>
</ul>


News from LabRulezLCMS Library - Week 30, 2024

<p><strong>In the week of July 29, the following webinars await you in the field of liquid phase and especially HPLC and LC/MS.</strong></p>
<blockquote>
<h4><a href="https://lcms.labrulez.com/webinars"><strong>👉 DETAILS AND REGISTRATION IN THE WEBINARS SECTION</strong></a></h4>
</blockquote>
<blockquote>
<p><strong>👉 Search and filter in the largest global database</strong>  with over <strong>3 500 GC, LC, MS and spectroscopy webinars</strong>.</p>
</blockquote>
<h5><strong>1. SCIEX: Excel strategies for mass spectrometry data analysis</strong></h5>
<ul>
<li>Tu, 30.7.2024 11:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/3857">Registration</a></li>
</ul>
<p>Elevate your analytical expertise with advanced techniques and workflows.</p>
<h5><strong>2. CTC Analytics: Advancing PFAS Analysis: Robotic Automation and Streamlined LC-MS Workflows</strong></h5>
<ul>
<li>We, 31.7.2024 09:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4137">Registration</a></li>
</ul>
<p>This webinar showcases the latest advancements in LC-MS workflows and robotic automation.</p>
<h5><strong>3. Waters Corporation: Exploring Enhanced Macromolecular and Nanoparticle Analysis through the Integration of DLS/ELS/SLS with the ZetaStar Instrument</strong></h5>
<ul>
<li>We, 31.7.2024 11:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4132">Registration</a></li>
</ul>
<p>The DynaPro ZetaStar instrument provides the capability for automated, unattended screening of a large range of sample and buffer conditions, which increases efficiency and reduces time to market.</p>
<h5><strong>4. Separation Science/SCIEX: PFAS Analysis in Food: A Robustness Study in Sensitivity and Stability</strong></h5>
<ul>
<li>We, 31.7.2024 11:30 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4112">Registration</a></li>
</ul>
<p>Learn how cutting-edge mass spec technology can co-exist with stability and robustness. It doesn’t have to be a compromise.</p>
<h5><strong>5. The Analytical Scientist/SCIEX: An approach to streamline and simplify the identification of crucial metabolites from targeted protein degraders</strong></h5>
<ul>
<li>We, 31.7.2024 15:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4110">Registration</a></li>
</ul>
<p>Fragment information from EAD and CID spectra were processed in a single result file to achieve confident structure assignment of and localization of metabolites.</p>
<h5><strong>6. Agilent Technologies: Analysis of Per- and Polyfluoroalkyl Substances in Different Media: Produce, Wastewater, and Air</strong></h5>
<ul>
<li>We, 31.7.2024 17:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4134">Registration</a></li>
</ul>
<p>This presentation will summarize analytical methods to determine PFAS concentrations in produce from the vicinity of a fluorochemical plant, wastewater, and air near wastewater treatment plants.</p>
<h5><strong>7. Waters Corporation: Structural characterization of functional polymers via light scattering and differential viscometry</strong></h5>
<ul>
<li>We, 31.7.2024 17:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4111">Registration</a></li>
</ul>
<p>This webinar will explore polymer characterization by multi-angle light scattering (MALS) and differential viscometry, coupled with size-exclusion chromatography or field-flow fractionation.</p>


 Webinars LabRulezLCMS Week 31/2024

<p><strong>Although he originally wanted to study mathematics, Tomáš Janoš eventually became an environmental epidemiologist. He completed his doctorate at RECETOX focusing on human biomonitoring, for which he received the Dean’s Award of the MU Faculty of Science. When he was in Spain, analyzing mortality due to heat and cold, he realized that he wanted to devote himself to studying the impact of extreme temperatures on human health. In the interview, he explains the origins of his interest in climate change, how such a topic is communicated to the public, and why he believes it is crucial for scientists in the Czech Republic to focus more on this issue.</strong></p>
<h5><strong>How did you become interested in climate change in your scientific work?</strong></h5>
<p>I was interested in climate change and the impacts of extreme temperatures on human health for most of my doctorate but I found space for this topic only at the very end. I noticed that in southern European countries, research on the impact of temperature on health is advancing, while Central and Eastern Europe is lagging. So, I thought exploring whether high and low temperatures have similar effects here would be interesting. At that time, I contacted colleagues from the Institute for Global Health in Barcelona, who have extensive experience with research on this topic. Then, I went to Spain with Czech data to learn how to process and analyze them. The topic intrigued me during my three months there, so I decided to write my own project and focus more on this direction.</p>
<h5><strong>In October 2023, a study on the relationship between mortality rates and extreme temperatures was published based on your work. Are you still dealing with this topic?</strong></h5>
<p>Yes, in connection with extreme temperatures, I also started to examine ambulance dispatches in the Czech Republic, which have not yet been explored on the national level in Europe. Such research examines different socio-economic groups and locations, which is important because temperatures vary from place to place. We have written a scientific article on this topic, which we hope to publish by the end of the year. Interestingly, not just elderly people, but also small children, teenagers, and young adults are at high risk. I also have a project studying the impact of short-term temperature fluctuations in combination with polluted air, such as smog, on the number of work accidents, especially among outdoor workers. I will be doing research for another two years, again with people from Barcelona, who are trying to create a European-wide database of work accidents, which already includes the Czech Republic, among others.</p>
<h5><strong>Is it difficult to get data for this type of research?</strong></h5>
<p>Data on deaths is obtained through excellent cooperation with the Institute of Health Information and Statistics of the Czech Republic. On the other hand, data on ambulance dispatches are much more difficult to obtain because of their sensitivity. We get them for certain territorial units, ambulance dispatches for example for districts, which is a terribly large territorial unit. If we went lower, we would get to the numbers of one, two dispatches a day, from which it would already be possible to deduce who it was specifically on a smaller territory. Also, not in all countries have data on ambulance dispatches collected and a database is made. Here, the information is again collected by the Institute of Health Information and Statistics of the Czech Republic from insurance companies, so a summary can be made. However, not in all countries does it work so comprehensively.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/RECETOX_In_the_next_years_climate_change_will_affect_everything_says_environmental_epidemiologist_Tomas_Janos_1_53337bc013.jpg" alt="RECETOX: In the next years, climate change will affect everything, says environmental epidemiologist Tomáš Janoš 1."/></p>
<h5><strong>So you work more with a summary of data, how do you find out that the dispatches were related to the temperature?</strong></h5>
<p>In general, attributing something to the weather is extremely difficult, something like that is not often even part of the diagnosis. Then there are epidemiological models that calculate with daily temperature and dispatches, and when they see some fluctuation that cannot be explained by anything else, they attribute it to the temperature. So we just get specific numbers and we do the calculations through models.</p>
<h5><strong>As for extreme temperatures in cities in general, can the aforementioned health risks be systematically prevented?</strong></h5>
<p>Definitely. Mortality studies for example show that in greener cities it is generally cooler by one to two degrees, which can save several lives a year. Furthermore, a network of fountains can be built, where a person can cool down. In Barcelona, for example, they have so-called climate refuges. It is a network of places where people from can hide in case of a heat wave. It’s nothing special, they are usually air-conditioned public places like supermarkets, libraries or museums, for which a map is created. Thanks to it, people find out where they can go in case of need and where they will be accepted. Therefore, it is important to inform the public and communicate the existence of refuges well, especially to populations which are at a higher risk, such as the elderly, and lower socioeconomic groups, for example by distributing leaflets. In Spain, they also created an early warning system, which several days in advance reports how high is the probability that due to high temperatures a certain number of people will die. Although it sounds morbid, it allows public institutions, such as hospitals and rescue services, to prepare for such a risk.</p>
<h5><strong>As for communication with the public, do you cooperate with other organizations or other public actors?</strong></h5>
<p>As an expert, I cooperate externally for example with Klimatická koalice, which is a platform of Czech non-profit organizations dealing with climate protection. One of their recent activities is the education of medical students in the field of climate change and how it can affect human health, because it is completely missing in the curriculum. The idea is that older people, for whom climate change poses the highest risk in terms of health, but at the same time tend to underestimate it the most, could draw information from doctors, who are a trustworthy authority for them.</p>
<h5><strong>And what does such cooperation bring to you as a scientist?</strong></h5>
<p>From my point of view as a scientist, it is often difficult to get the information to the right place where it will have an effect. Organizations like Klimatická koalice, Fakta o klimatu or the Institute for Czech Policy EUROPEUM help me a lot in this. When we published the study, thanks to the fact that I sent the information about it to everyone I knew would be interested in it, several public or media outputs were created. I probably wouldn’t be able to get it into awareness like this myself.</p>
<h5><strong>So do you have to initiate the first dissemination of information yourself?</strong></h5>
<p>Yes, we as scientists are not pushed into popularizing science much. It is usually more our own interest and it is not part of our performance. Communication is important and should be taken care of. In science, we often pat ourselves on the back, what a great article we published, but when you come to ordinary people outside the scientific sphere, they are interested in information, not the impact of the journal. Of course, at the beginning there must be a quality scientific study, but the actual effect should not be forgotten. Another thing is that it is difficult to communicate a complex problem well and convey it in a few sentences. To do it well, you need to educate yourself. But in practice, there is no time to do either.</p>
<h5><strong>What is it like to communicate the topic of climate change from the perspective of science?</strong></h5>
<p>There is definitely interest in the climate among the public, but when you say climate, it acts like a red rag. It evokes in people things that they will not be able to do or something for which others will condemn them. Moreover, I am afraid that over time it will rather worsen. At the same time, I think that people are interested in climate protection and the environment, we are just at it again, that it is necessary to communicate it all better.</p>
<h5><strong>How does the scientific community react to the topic of climate change? Is there interest there too?</strong></h5>
<p>I feel that the interest is primarily abroad so far. The impacts of it probably do not affect the Czech Republic so much yet, but it certainly awaits us. In the next fifty years, climate change will affect everything, including environmental epidemiology. I am dealing with a very limited section of the whole issue, but there are many more aspects. Through new invasive species, it will be necessary to change the way pesticides are used, there will be an increase in the incidence of infectious diseases, floods, cloudbursts, the change will affect air research, food safety or migration. We should not close our eyes to such a complex and difficult to explain problem as climate change. Whole research groups are devoted to it at foreign institutes, so the Czech Republic should not miss the boat.</p>


In the next years, climate change will affect everything, says environmental epidemiologist Tomáš Janoš.

<h3><strong>About us</strong></h3>
<p>Our laboratory is equipped with high-end mass spectrometry instruments, which offers services in field of <strong>PROTEOMICS</strong> and <strong>METABOLOMICS</strong>. All our services are available for everybody from the academic and non-academic areas.</p>
<h5><a href="https://www.biocev.eu/en/services/omics-mass-spectrometry-core-facility.6#core-facility-services"><strong>Our Services:</strong></a></h5>
<ul>
<li><strong>Preparation of samples</strong> for analysis (cells, body fluids, tissues, plants etc.)</li>
<li><strong>Targeted</strong> or <strong>untargeted</strong> <strong>proteomics</strong> and <strong>metabolomics</strong> analysis</li>
<li><strong>Data analysis</strong> and basic statistical evaluation</li>
<li><strong>Consultation</strong> of experimental design and the results</li>
</ul>
<h5><strong>Proteomics:</strong></h5>
<p>We are modern well equipped laboratory with the technical background able to perform most of the currently used <a href="https://www.biocev.eu/en/services/omics-mass-spectrometry-core-facility.6/untargeted-proteomics.24?t=s"><strong>untargeted</strong></a> and <a href="https://www.biocev.eu/en/services/omics-mass-spectrometry-core-facility.6/targeted-proteomics.25?t=s"><strong>targeted</strong></a> proteomic measurements. We provide full proteomics service, including protein isolation from the supplied sample to evaluation and consultation of the measured data. Since 2015, we handle approximately 300 orders per year (roughly 3000 samples). Results based on measurements from our laboratory were used in dozens of publications. To consult your plan, please contact Karel Harant (karel.harant@natur.cuni.cz) or Pavla Talacko (pavel.talacko@natur.cuni.cz).</p>
<h5><strong>Metabolomics:</strong></h5>
<p>As a service, we provide <a href="https://www.biocev.eu/en/services/omics-mass-spectrometry-core-facility.6/targeted-metabolomics.26?t=s"><strong>targeted</strong></a> and <a href="https://www.biocev.eu/en/services/omics-mass-spectrometry-core-facility.6/untargeted-metabolomics.30?t=s"><strong>untargeted</strong></a> analysis of small molecules. Thanks to the combination of equipment for <strong>LC-MS</strong> and <strong>GCxGC-MS</strong>, it is possible to measure a wide range of small molecules. We use several types of <strong>C18</strong> and <strong>HILIC</strong> stationary phase columns on LC. For GC, we have various columns for different types of analytes. Individual measuremnts must always be consulted in advance, an individual approach and method must be chosen for each group of molecules. Please contact Olga Součková (souckoo@natur.cuni.cz) for LC-MS or Petr Žáček (zacek@natur.cuni.cz) for GCxGC-MS.</p>
<blockquote>
<p><strong>All our services are available for everybody from the academic and non-academic areas.</strong></p>
</blockquote>
<blockquote>
<p><strong>Contact us before you start your first experiment: +420 325 873 925!</strong></p>
</blockquote>
<blockquote>
<p><strong>23.7.2024 Waiting time from “sample to result” is approximately 6-8 weeks.</strong></p>
</blockquote>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_cover_image_7cb6de4462.jpg" alt="BIOCEV: BIOCEV OMICS Mass Spectrometry Core Facility"/></p>
<h3><strong>Services</strong></h3>
<ul>
<li>Preparation of samples for analysis</li>
<li>Untargeted and targeted proteomics</li>
<li>Untargeted and targeted metabolomics</li>
<li>Data analysis and basic statistical processing</li>
<li>Consultation of experiment design and measured data</li>
</ul>
<h4><strong>Untargeted proteomics</strong></h4>
<h5><strong>Up to 8000 identified proteins in one injection.</strong></h5>
<p>A basic type of proteomic experiment. Complete lysate is digested with trypsin. The resulting peptides are desalted and separated on a reverse phase column. Due to the low amount of proteins and the high complexity of the sample, liquid chromatography is currently most often used in nanoflow - hundreds of nanoliters per minute. Liquid chromatography is directly connected to the electrospray of the Orbitrap Fusion or Orbitrap Ascend mass spectrometer. The mass spectrometer measures alternately in two modes: MS¹, where peptide masses are measured in the Orbitrap with high resolution and accuracy, and MS², in which peptides selected from the previous MS¹ scan are fragmented. These are measured either again in the Orbitrap or in the ion trap. The ion trap provides lower accuracy and resolution than the Orbitrap, but is faster and more sensitive.</p>
<blockquote>
<p><strong>We offer untargeted proteomics measurement and analysis of post-translational modifications in different types of samples (cells, tissues, body fluids, plant samples, etc.).</strong></p>
</blockquote>
<blockquote>
<p><strong>Our newest service is &quot;Thermal proteome profiling (TPP)&quot; that allows you direct detection of drug-protein interactions in living cells.</strong></p>
</blockquote>
<h5><strong>Examples of analyses:</strong></h5>
<ul>
<li>LFQ (label free quantification)</li>
<li>TMT (tandem mass tags)</li>
<li>TPP (Thermal proteome profiling)</li>
<li>phosphoproteome profiling</li>
<li>pull-down experiments</li>
</ul>
<h5><strong>Tips for sample handling:</strong></h5>
<ul>
<li>do not use trypsin for cell harvesting</li>
<li>inform us about presence of detergent</li>
<li>always keep in mind same protein loading for pull-down experiments (eg. Co-immunoprecipitation)</li>
<li>do not use phosphatase inhibitors for phosphoproteomic experiments</li>
</ul>
<h4><strong>Targeted proteomics</strong></h4>
<h5><strong>Accurate quantification of selected proteins.</strong></h5>
<p>Method aims to validate the results from an untargeted approach. It is performed on a triple quadrupole in SRM mode or using the MRM method on an Orbitrap. It is an an alternative approach to common techniques such as western blot. The advantage of this approach is the possibility to analyze several proteins (dozens) at once during one injection. This eliminates the problem of finding suitable antibodies.</p>
<blockquote>
<p><strong>The targeted proteomics service is always project specific and we offer it after prior meeting with the customer.</strong></p>
</blockquote>
<p>Parallel analysis of peptides labeled with heavy amino acids is essential. These serve as an internal standards.</p>
<p>The amount of proteins that can be targeted in one injection using a triple quadrupole, is strongly dependent on the concentration of the target proteins in the sample. The lower the expression of the target proteins, the less it is possible to analyze them in one injection due to the need for higher loading times. Information of fragmentation properties of targeted peptides is also important. This is usually obtained from an untargeted experiment, which should precede the targeted proteomic analysis. If the protein of interest was not detected during an untargeted experiment, then its targeted analysis is very difficult. However, in some cases fragmentation information can be obtained from publicly available databases.</p>
<h5><strong>Tips for sample handling:</strong></h5>
<ul>
<li>do not use trypsin for cell harvesting</li>
<li>inform us about presence of detergent</li>
<li>always keep in mind same protein loading for pull-down experiments (eg. Co-immunoprecipitation)</li>
<li>do not use phosphatase inhibitors for phosphoproteomic experiments</li>
</ul>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_Targeted_proteomics_1_f0605d8efc.jpg" alt="BIOCEV: Introducing BIOCEV OMICS Mass Spectrometry Core Facility - Targeted proteomics."/></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_Targeted_proteomics_2_f1af260d27.jpg" alt="BIOCEV: Introducing BIOCEV OMICS Mass Spectrometry Core Facility - Targeted proteomics."/></p>
<h4><strong>Untargeted metabolomics</strong></h4>
<p>The goal of untargeted metabolomics is to cover the widest possible spectrum of metabolites present in the sample, their identification, and quantification. The development of this approach was made possible by the recent advances in instrumentation and computing. Our laboratory equipment enables non-targeted analyses by liquid and gas chromatography.</p>
<blockquote>
<p><strong>We offer untargeted analyses of metabolites in various biological matrices and basic statistical evaluation of the data (Figure 2, 3, 4).</strong></p>
</blockquote>
<blockquote>
<p><strong>Our newest service is stable isotope tracing (Figure 1).</strong></p>
</blockquote>
<p>HPLC-MS/MS (Figure 2): Analyzes are performed on Thermo Scientific equipment on an Ultimate 3000 liquid chromatograph coupled to an Orbitrap Fusion mass detector. The measured data are evaluated by the Compound Discoverer software.</p>
<p>GCxGC-MS (Figure 3): Analyzes are performed on a two-dimensional comprehensive chromatograph connected to a Pegasus 4D mass detector. We evaluate the data in ChromaTOF v4.5 software.</p>
<p>The liquid chromatography method covers non-volatile substances, generally polar, soluble in water, and polar organic solvents (methanol, acetonitrile...). The gas chromatography method is more suitable for analyzing stable volatile non-polar substances up to a weight of approx. 1000 Da. The range of measured substances can be increased for both methods eg., by chemical modifications (derivatization) of the analyzed molecules, which adjust their polarity and volatility (for GC) and/or stability (for LC). We choose a suitable technique or a combination of several techniques based on prior consultation with the customer.</p>
<p>The untargeted analysis results in a list of substances found in the samples, a proposal of probable structures, and an indication of the quantity of individual compounds. We also provide a basic statistical evaluation focusing on looking for differences between the tested sample groups (Figure 4).</p>
<h5><strong>Tips for sample handling:</strong></h5>
<ul>
<li>do not use phosphate buffers in the sample</li>
<li>inform us about sample type, growth medium, chemicals used, etc.</li>
</ul>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_Untargeted_metabolomics_Fig_1_11750e6992.jpg" alt="BIOCEV: Introducing BIOCEV OMICS Mass Spectrometry Core Facility - Untargeted metabolomics Fig. 1."/></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_Untargeted_metabolomics_Fig_2_5ca1521705.jpg" alt="BIOCEV: Introducing BIOCEV OMICS Mass Spectrometry Core Facility - Untargeted metabolomics Fig. 2."/></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_Untargeted_metabolomics_Fig_3_f4f1050fc5.jpg" alt="BIOCEV: Introducing BIOCEV OMICS Mass Spectrometry Core Facility - Untargeted metabolomics Fig. 3."/></p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_Untargeted_metabolomics_Fig_4_b3e198dbc9.jpg" alt="BIOCEV: Introducing BIOCEV OMICS Mass Spectrometry Core Facility - Untargeted metabolomics Fig. 4."/></p>
<h4><strong>Targeted metabolomics</strong></h4>
<p>Targeted metabolomics includes analyses of selected metabolites, which are then detected selectively and with greater sensitivity than applying an untargeted approach. It is also possible to quantify substances both relatively and absolutely. In the case of absolute quantification, it is necessary to supply a suitable labeled analog of the determined substance.</p>
<blockquote>
<p><strong>We offer analysis of primary cellular metabolites - see List of substances.</strong></p>
</blockquote>
<blockquote>
<p><strong>We analyze metabolites in tissues, cell pellets, incubation media, and body fluids (plasma, urine...).</strong></p>
</blockquote>
<blockquote>
<p><strong>We also offer the possibility of developing a method for the analysis of substances that are not in the attached list or for other matrices.</strong></p>
</blockquote>
<p>The attached list contains substances with the analysis of which we have experience. We adapt each method to the type of experiment and matrix. We can develop a method for any substance or group of substances capable of being detected by liquid and gas chromatography techniques (both connected to a mass detector or a UV detector in liquid chromatography). In the case of the development of a new method, it is necessary to supply the standards of these substances.</p>
<h5><strong>Tips for sample handling:</strong></h5>
<ul>
<li>do not use phosphate buffers in the sample</li>
<li>inform us about sample type, growth medium, chemicals used, etc.</li>
</ul>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/BIOCEV_Introducing_BIOCEV_OMICS_Mass_Spectrometry_Core_Facility_Targeted_metabolomics_List_of_substances_a6a4198b34.jpg" alt="BIOCEV: Introducing BIOCEV OMICS Mass Spectrometry Core Facility - Targeted metabolomics: List of substances."/></p>
<h3><a href="https://www.biocev.eu/en/services/omics-mass-spectrometry-core-facility.6#core-facility-equipment"><strong>Equipment</strong></a></h3>
<h4><strong>Mass spectrometers</strong></h4>
<h5><strong>Orbitrap Ascend</strong></h5>
<ul>
<li><a href="https://lcms.labrulez.com/library?instrumentationItems=31-32-33-30&amp;mainauthorItems=3&amp;search=Ascend"><strong>Application in the LabRulezLCMS library</strong></a></li>
</ul>
<p>Thermo Scientific Orbitrap Ascend Tribrid mass spectrometer, offering new capabilities for multiplexed proteomics and native protein characterization. The mass spectrometer enables improved sample throughput, versatility and ease-of-use — producing high quality data with simplicity. More samples can be analyzed at lower concentrations, enabling faster, more sensitive analysis, and macromolecule experiments, that were not possible before, can now be achieved. The new Auto-Ready ion source for calibration maximizes convenience, allowing the user to spend more time on the results, and less time on instrument set-up.</p>
<h5><strong>Orbitrap Fusion</strong></h5>
<ul>
<li><a href="https://lcms.labrulez.com/library?instrumentationItems=31-32-33-30&amp;mainauthorItems=3&amp;search=Fusion"><strong>Application in the LabRulezLCMS library</strong></a></li>
</ul>
<p>Mass spectrometer combining Quadrupole, Ion trap and Orbitrap. The quadrupole is used as a mass filter for the selection of precursors, after which the instrument branches and the ions can travel either to the Orbitrap - a very accurate and high-resolution mass analyzer that uses the Fourier transform to determine their mass, or to the collision cell, where they can be fragmented. From there, the path leads either back to the Orbitrap or further to the linear ion trap. This serves as the second mass analyzer in the device. It is less accurate and low-resolution, but provides greater sensitivity and the possibility of ion fragmentation. Fragmentation products can be isolated in the trap and fragmented again. This enables analysis in MS³ and even higher levels of fragmentation.</p>
<h5><strong>TSQ Quantiva Triple Quadrupole Mass Spectrometer</strong></h5>
<ul>
<li><a href="https://lcms.labrulez.com/library?instrumentationItems=31-32-35&amp;mainauthorItems=3&amp;search=Quantiva"><strong>Application in the LabRulezLCMS library</strong></a></li>
</ul>
<h5><strong>Leco - Pegasus® 4D GCxGC-TOFMS</strong></h5>
<ul>
<li><a href="https://gcms.labrulez.com/library?instrumentationItems=3-13-2&amp;mainauthorItems=24&amp;search=4D"><strong>Application in the LabRulezGCMS library</strong></a></li>
</ul>
<h4><strong>Liquid chromatography</strong></h4>
<ul>
<li>nano LC Thermo Dionex Ultimate 3000</li>
<li>LC Thermo Dionex Ultimate 3000</li>
</ul>
<h4><strong>Sample preparation</strong></h4>
<ul>
<li>KingFisher Flex</li>
<li>vacuum concentrator</li>
<li>Low flow fraction collector - Spider</li>
<li>Bioruptor pico - sonication bath</li>
</ul>
<h4><strong>Software</strong></h4>
<ul>
<li>Spectronaut 19</li>
<li>FreeStyle</li>
<li>ChromaTOF 4.5</li>
<li>Proteome Discoverer 2.2</li>
<li>Scaffold Q+S 4.6.1</li>
<li>Compound Discoverer 3.3</li>
<li>TraceFinder</li>
</ul>
<h5><strong>Software - Freeware</strong></h5>
<ul>
<li>LipidHunter</li>
<li>MaxQuant</li>
<li>Perseus</li>
<li>Skyline</li>
</ul>
<h3><a href="https://www.biocev.eu/en/services/omics-mass-spectrometry-core-facility.6#core-facility-team"><strong>Team</strong></a></h3>
<h5><strong>Mgr. Karel Harant</strong></h5>
<ul>
<li>Head of Proteomic Core Facilty</li>
</ul>
<h5><strong>Mgr. Pavel Talacko</strong></h5>
<ul>
<li>Non-targeted proteomics, targeted proteomics</li>
</ul>
<h5><strong>RNDr. Petr Žáček, Ph.D.</strong></h5>
<ul>
<li>GC / MS specialist, small molecule analysis</li>
</ul>
<h5><strong>Mgr. Veronika Ševců</strong></h5>
<ul>
<li>researcher, preparation of proteomic samples</li>
</ul>
<h5><strong>RNDr. Petr Žáček, Ph.D.</strong></h5>
<h5><strong>Mgr. Veronika Ševců</strong></h5>
<ul>
<li>researcher, preparation of proteomic samples</li>
</ul>
<h5><strong>Ing. Olga Součková, Ph.D.</strong></h5>
<ul>
<li>LC/MS specialist, small molecule analysis</li>
</ul>


Introducing BIOCEV OMICS Mass Spectrometry Core Facility

<p><strong>Amyotrophic lateral sclerosis, ALS for short, is a mysterious neurodegenerative disease that is almost always fatal. A consortium of researchers led by the Technical University of Munich (TUM) has systematically investigated the underlying molecular mechanisms of ALS. Among other things, the team discovered that ALS can be divided into subtypes. Depending on the subtype, different drugs could be effective. There are also clear differences in the molecular processes when comparing men and women.</strong></p>
<p>The molecular processes in the body that cause ALS patients to increasingly lose control of motor functions are still poorly understood. Previous studies have been limited to individual aspects of the underlying molecular processes. A consortium led by Prof. Paul Lingor, a neurologist at TUM, has investigated ALS using a so-called &quot;multi-omics&quot; approach. The researchers mapped both coding and non-coding RNA molecules and the entirety of the proteins.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/TUM_Mojan_Parvaz_Insight_into_the_molecular_mechanisms_of_ALS_There_are_hardly_any_drugs_against_ALS_A_new_study_shows_that_a_substance_acting_on_the_MAPK_signaling_pathway_6f7450013b.jpg" alt="Technical University of Munich /  Mojan Parvaz: There are hardly any drugs against ALS. A new study shows that a substance acting on the MAPK signaling pathway may help: After treatment with trametinib, mouse nerve cells (blue) survived better than without."/></p>
<h4><strong>Four subtypes</strong></h4>
<p>A key finding of the study is that ALS can be roughly divided into four subtypes. <em>&quot;You can&#39;t distinguish between these variants based on the clinical symptoms,&quot;</em> says Paul Lingor, who, together with other researchers is part of the <a href="https://www.synergy-munich.de/"><strong>SyNergy Cluster of Excellence</strong></a> investigating neurodegenerative diseases. <em>&quot;However, very different things happen at the molecular level. This means that an active substance that is ineffective in one ALS subtype may well be helpful in another. Previous clinical studies were only able to look at the effects across all patients and may not have identified substances effective for an individual subtype.&quot;</em></p>
<p>While in one common subtype genes associated with inflammatory processes and immune responses were affected, in another there were mainly disturbances in the transcription of DNA into RNA molecules. In two others, different signs of oxidative stress were found in the cells. The researchers assume that the ALS subtype may change over the course of the disease.</p>
<h4><strong>Promising drug identified</strong></h4>
<p>Men develop ALS around 1.2 times more frequently than women. The breakdown of the molecular processes also revealed clear differences between the sexes. While the four subtypes appear to occur equally frequently in both sexes, the researchers found a significantly larger number of altered gene products in men. From the researchers&#39; point of view, this could mean that men and women will have to be treated differently in future.</p>
<p>Through the multi-omics analysis, the researchers also identified a signaling pathway that could be a particularly suitable target for new drugs against ALS. <em>&quot;This signaling pathway, MAPK, is well described in neurobiology and plays a role in various, although by no means all, processes in ALS,&quot;</em> says Prof. Stefan Bonn, co-last author of the study and Director of the Institute for Medical Systems Biology at the University Medical Center Hamburg Eppendorf (UKE). From the researchers&#39; point of view, it would therefore be promising to repurpose an approved cancer drug that acts on MAPK for ALS.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/TUM_Klinikum_rechts_der_Isar_Thomas_Einberger_Insight_into_the_molecular_mechanisms_of_ALS_Prof_Paul_Lingor_is_the_head_of_the_consortium_that_conducted_the_study_98122db927.jpg" alt="Technical University of Munich / Klinikum rechts der Isar / Thomas Einberger: Prof. Paul Lingor is the head of the consortium that conducted the study."/></p>
<h4><strong>Basis for future studies</strong></h4>
<p>The study is based on tissue samples from deceased ALS patients and additional investigations using mouse models of the disease. <em>&quot;An important next step is to find a way to determine the ALS subtype of patients while they are still alive - we are currently working on this,&quot;</em> says Paul Lingor. <em>&quot;We believe that our study made an important contribution in the search for causes and therapies for ALS. Our findings have brought us a good deal closer to a more personalized and therefore more effective therapy.&quot;</em></p>


Insight into the molecular mechanisms of ALS

<p><strong>In the week of August 5, the following webinars await you in the field of liquid phase and especially HPLC and LC/MS.</strong></p>
<blockquote>
<h4><a href="https://lcms.labrulez.com/webinars"><strong>👉 DETAILS AND REGISTRATION IN THE WEBINARS SECTION</strong></a></h4>
</blockquote>
<blockquote>
<p><strong>👉 Search and filter in the largest global database</strong>  with over <strong>3 500 GC, LC, MS and spectroscopy webinars</strong>.</p>
</blockquote>
<h5><strong>1. Thermo Fisher Scientific: Navigating changes in regulated software environments</strong></h5>
<ul>
<li>Tu, 6.8.2024 08:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4174">Registration</a></li>
</ul>
<p>Changing regulatory landscapes, observations, and considerations when aligning software records with ALCOA+ principles.</p>
<h5><strong>2. SCIEX: SCIEX OS software summer school - Compound optimization</strong></h5>
<ul>
<li>Tu, 6.8.2024 11:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4156">Registration</a></li>
</ul>
<p>Join us for our summer school series dedicated to enhancing your proficiency with SCIEX OS software.</p>
<h5><strong>3. Phenomenex: Solid Phase Extraction Introduction and Theory</strong></h5>
<ul>
<li>Tu, 6.8.2024 19:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4159">Registration</a></li>
</ul>
<p>Understand the benefit of using SPE than other sample preparation techniques.</p>
<h5><strong>4. Agilent Technologies: Analytical Strategies for Uncovering the Biological Burden of &quot;Forever Chemicals&quot;</strong></h5>
<ul>
<li>We, 7.8.2024 17:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4135">Registration</a></li>
</ul>
<p>Progress and remaining challenges in using high-resolution mass spectrometry (HRMS) to comprehensively capture the total burden of PFASs accumulating in living organisms. </p>
<h5><strong>5. Thermo Fisher Scientific: New ways of targeted translational small molecules quantification</strong></h5>
<ul>
<li>Th, 8.8.2024 11:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4152">Registration</a></li>
</ul>
<p>In this free webinar, Hector shares preliminary data and insights into the critical role of lipids in biochemical processes.</p>
<h5><strong>6. Technology Networks/Bruker: Applying Spatial Multiomics to Degenerative Diseases and Cancer</strong></h5>
<ul>
<li>Th, 8.8.2024 17:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4183">Registration</a></li>
</ul>
<p>Our speaker will discuss how new MALDI workflows can be used to analyze lipids in degenerative disease and Alzheimer’s models, providing more depth to lipid analysis and contextualizing lipid distribution.</p>
<h5><strong>7. Phenomenex: HPLC Method Development: Practical Approaches for Identifying Equivalent and Orthogonal Columns</strong></h5>
<ul>
<li>Fr, 9.8.2024 19:00 CEST</li>
<li><a href="https://lcms.labrulez.com/webinar/4087">Registration</a></li>
</ul>
<p>Learn about physical and chemical properties of common reverse phase stationary phases, Find an understanding and recieve steps for stationary phase selection.</p>


 Webinars LabRulezLCMS Week 32/2024

<p><strong>Although plastics don’t have the best reputation at present, they have fascinating properties. Modern society cannot make do without them. We all use them, and we’re not going to stop using plastics just like that. Why? The answer to this question follows in this interview with Professor Jan Merna, head of <a href="https://lcms.labrulez.com/companies/11">UCT Prague</a>’s Department of Polymers. Merna also discusses trends in polymer research, new approaches to 3D printing, and why biodegradable polymers are not the game changer they might seem to be at first glance.</strong></p>
<h5><strong>People commonly associate polymers with plastics, which do not have the best reputation with some in the general public. Why did you choose to study polymers in your professional life?</strong></h5>
<p>I became interested in polymers as far back as high school because they are cutting-edge materials. The study of polymers is actually the youngest branch of chemistry, next to the organic and inorganic branches. Just last year marked 100 years since chemists gained an understanding of the structure of polymers. There was hot discussion in the early days of the field. There were no polymer chemists, so a couple of organic chemists came up with the initial idea to create a specialty in this area. Hermann Staudinger, who demonstrated that polymers are composed of high molar mass macromolecules, had to struggle for a long time against the entire chemistry community at the time to show that polymers are not clusters of small molecules but are huge macromolecules. Most renowned chemists thought that such large molecules could not be stable and must be clusters. They were mistaken, though Staudinger waited over 30 years after his initial discoveries for the Nobel Prize.</p>
<p>What I like about polymers and modern materials is that they have a range of different applications and that the topic itself is complex. In organic chemistry, we often synthesize a new substance, describe it, and that’s more or less the end of the process. But for polymer chemists, the polymer synthesis is often just the beginning of research work, because we are interested in the material properties of a synthesized substance and investigating what a substance might be good for in real life. Lately, we are also thinking more about end-of-life for materials; how to deal with polymer waste.</p>
<p><strong>You mean recycling?</strong></p>
<p>Yes, this is a very important topic. We in Europe collect most of our plastic waste and not much of it ends up in the environment, but the problem arises in other parts of the world where there is poor waste management. If plastics get into nature, one of the properties of polymers is that they are very resistant to degradation and can survive in the environment for hundreds of years before disintegrating.</p>
<p>Actually, the optimal solution would be to develop better systems for collecting and reusing plastic waste. This presumes careful sorting into individual types of plastic, because if we don’t sort properly, just mix different kinds of plastics together, melt them, and make new products, the resultant outputs won’t have good properties. However, proper sorting is not only difficult, but it is also expensive. Plastic recycling also can’t be performed on an infinite loop, because repeated melting degrades the polymers involved and there is a limited number of cycles before the polymers become unusable. That’s why current research is focusing on finding alternative to mechanical recycling.</p>
<p><strong>Which is?</strong></p>
<p>The crucial challenge for our field is finding an economical and energetically reasonable way how to get to monomers, which are the primary raw materials from which virgin polymer can also be produced. So far, there are solutions for selected polymers, e.g. polyethylene terephthalate or polymethyl methacrylate (that is, plexiglass), but the vast majority of these are polymers that are not used broadly. We would need to find viable and cheap solutions for polyethylene and polypropylene. Unfortunately, there is no viable cleavage site in the structures of polyethylene and polypropylene, and current technologies such as pyrolysis are not very selective.</p>
<p>Another research direction is the quest for new monomers for the production of polymers that could then be easily degraded, i.e. recycled chemically. The problem, however, is that since the 1970s, no new polymers have gained ground in the marketplace, mostly for economic reasons. We will see if a requirement for good degradability would hearken change and if these kinds of new polymers might have competitive properties in terms of strength, ductility, processing stability, and so on.</p>
<p><strong>Does plastic waste in nature, despite being ugly, have other problems?</strong></p>
<p>In general, polymers are non-toxic inert substances and are biologically tolerated. They do not harm us on their own and are not toxic. Body implants are made from polymers; tissue substitutes are made from silicone. We store blood for transfusions in PVC bags softened with phthalates. What we don’t know for sure is whether polymers cause any health risks in the form of small particles.</p>
<p><strong>For example?</strong></p>
<p>There is an existing hypothesis that microplastics can act as carriers of pathogens, but this risk exists for all microparticles in the environment. We have been living with synthetic plastics for at least 70 years, so microplastics in the environment are not a recent phenomenon. In the past, thought, polymer products were not stabilized as well as they are now. They used to decompose over shorter intervals, and so-called secondary microplastics were formed more easily (but from far fewer plastics were produced). The first mention of finding microplastics in oceans dates back to the 1970s, but this was not a fashionable topic of investigation back then. Due to plastic non-toxicity, the WHO does not recommended monitoring microplastics in water. Water purification technologies, however, can be highly effective in removing any particles, including microplastics.</p>
<p><strong>What do you think about the fact that most plastics collected in yellow recycling bins across the Czech Republic end up in incinerators?</strong></p>
<p>Fine by me. From a chemist’s point of view, this is definitely a better scenario than being out in the environment or in a landfill. Of course, I’m talking about plastics, which are difficult to recycle. Most polymers are made from oil, and human being burn 90% of oil straight away. So if plastics could serve as an intermediate material product and we could get part of the energy we invested in production back, why not? The exhaust fumes from incineration of most common polymers are not toxic and are similar to those of burning gasoline, i.e. made of carbon dioxide and water.</p>
<p><strong>One of current research trends is the production of biodegradable polymers.</strong></p>
<p>Yes, but even in this case, one must note that even if a polymer breaks down into something harmless in nature after some time, we lose all the energy we had put into its production.</p>
<p>I believe that for biodegradable polymers, a much better scenario for the end of a product’s life cycle would be to collect and recycle them, or, if recycling’s not possible, to incinerate them. For polymers from renewable sources, this would achieve a neutral carbon balance. If we can collect plastic waste, it doesn’t matter if it’s biodegradable or very stable since we still can transform it into something.</p>
<p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/VSCHT_Ze_cast_plastu_konci_ve_spalovnach_Za_me_v_poradku_Jan_Merna_76e58abc1f.jpg" alt="UCT Prague: Jan Merna."/></p>
<p><strong>Are there any other hot topics for polymer researchers?</strong></p>
<p>Right now, new 3D printing technologies that naturally lend themselves well to small-scale production are very hot. Specifically, I am referring to reactive 3D printing, where polymerization takes place directly during production (printing), where the resulting product has significantly better properties than what’s possible using classic 3D printing technology from polymer strings. We are investigating this at UCT Prague as well.</p>
<p><strong>How do you polymerize during the printing process?</strong></p>
<p>We use light, for example. We have a bowl with a transparent bottom, pour a monomer into it, and the light where it passes through starts the polymerization process. Then we move the product a little higher and the monomer will again flow under the product under development, and so on, until a completely compact, homogeneous product is created.</p>
<p><strong>Can you also produce polymers that can react to external stimuli?</strong></p>
<p>Yes, this is also an attractive direction for research. For example, we have polymers which macromolecules, when heated, change shape and, for example, pack into a tighter conformation. Macroscopically, this manifests itself in the form of shrinkage that we can use as a mechanical element, a trigger or a valve. The stimuli can be different: ​​temperature, pH, or the presence of a specific chemical. There’s the potential for use in detectors or sensors.</p>
<p><strong>Your department is historically connected to the topic of hydrogels. Is there still room for development in this direction?</strong></p>
<p>Hydrogels belong to the group of materials that are attractive because they can be used in medical applications. Due to the softness and pliability of hydrogels, they are also used as substitutes for human soft tissue, beside traditional use as contact lenses developed by Otto Wichterle. Soft tissues are composed of natural protein macromolecules, i.e. they are also polymers, just perfectly produced by nature.</p>
<p><strong>You are particularly interested in research of catalytic polymerizations. What is that?</strong></p>
<p>You’re referring to coordination polymerization, but we ourselves also use the term “catalytic polymerization” for better comprehension. For most polymerizations, we need a substance that forces a monomer to transform into a polymer. In catalytic polymerizations, the agent that forces this transformation is the catalyst. We currently use such processes to produce the majority of polyethylene and polypropylene that together comprise the majority of plastics. The basic procedure has been around for decades but was initially unviable. As catalysts gradually developed, production increased, and today, these basic polymers are produced so well and so efficiently in terms of pricing and properties that they are replacing other polymers used in traditional applications.</p>
<p><strong>Can you give us an example?</strong></p>
<p>For the production of foils, e.g. for shopping bags, softened polyvinyl chloride was used most often in the past. Polyethylene is now used because not only is it cheaper, but its production is also more ecological. Modification of polyethylene and polypropylene properties for other application is definitely still a promising direction of research.</p>
<p>In academic research, the search for even more active catalysts is not our greatest concern because we can produce a lot of polymers cheaply enough. Instead, current research is directed towards the possibilities of depolymerization and investigating whether we will be able to selectively split a polymer into pieces and turn it into new material. In our research group, we focus on chemical modifications of polyethylene and we use one specific type of catalyst, the so-called chain walking catalysts. In the case of classic industrial catalysts, a monomer molecule sticks to the end of a growing macromolecule, and this is how the chain lengthens linearly. The catalysts we use are extraordinary in that they can jump back and forth along a polymer chain and start its growth again from a given part of the chain. The result is a macromolecule that is not “straight” but highly branched, and this completely changes its properties.</p>
<p><strong>How?</strong></p>
<p>For example, polyethylene and polypropylene are typical plastics and are hard materials, but if we branch them, we can make them into materials that have the same properties as rubber. Our next endeavour is to build polar groups into polyethylene chains. This is one of the biggest challenges in current catalysis. Fortunately, our catalysts are toleranteven to polar substrates, and this lets us to prepare special polar-non-polar macromolecules from which polymer nanoreactors can be constructed, to name one example. This means we are moving from commodity materials to chemical specialties.</p>
<p><strong>Does your research group currently collaborate with commercial partners?</strong></p>
<p>We have collaborated with Synthos for a long time. Most recently, as part of a two-year project, we jointly developed a new type of elastomer not based on butadiene polymers (normally used to make rubber) but on cheaper polymers based on ethylene.</p>
<p><strong>You said that the vast majority of polymers are made from petroleum. How much plastic is produced from renewable raw materials?</strong></p>
<p>Less than 1%, and the production costs are usually higher, so an increase in production is not very rapid. This is nicely described in the article “How green are green plastics?” To make a long story short, we use more energy to make environmentally degradable polymers than to make synthetic polymers. Which may not be problematic in principle, as long as fossil fuel energy isn’t required. So if we get to a future scenario in which non-fossil fuel energy sources are not a problem for us, this is one of possible path forward. We are still far from this ideal, however.</p>
<p>For the future, it should just be necessary to shift our point of view about options. In our group, we have investigated the use of carbon dioxide as a starting raw material for preparing polymers, for example. We overcame CO2’s low reactivity by adding a second, more reactive monomer and a suitable catalyst. The result was polycarbonates, which are otherwise produced from highly toxic phosgene. This kind of chemistry is not only more sustainable, but it can improve safety. So far, however, catalysts are not effective enough for industrial scale production, but this also used to be the for the aforementioned ethene polymerization catalysts in the beginning of their development.</p>
<p><strong>You have been head of the Department of Polymers for over two years. Where do you want to lead the department?</strong></p>
<p>I have no desire to tell people what to do. On the contrary, I would like them to be as independent as possible in their research. As a leader, what I can and want to influence is what kind of people will work here. We are currently witnessing a generational transition. Half of my colleagues are at an age when they wouldn’t have to show up tomorrow if they didn’t want to. Fortunately, they are kind-hearted, helping us here and passing on their experience to younger colleagues. It’s up to me to find us quality replacements for the future.</p>
<p>At first, I was sceptical that this could be possible, because we all know how basic table salaries are set here at UCT Prague. How to tell a potential candidate from abroad that their salary will be only higher if they find grant funding? Just 100 km away from Prague, candidates can get an adequate guaranteed salary (several times higher than here) for the same work. The number of students studying in materials programs is not large enough to ensure a big enough pool of doctoral students to meet our near-term needs for qualified research staff.</p>
<p>Nevertheless, we managed to recruit one former graduate who had completed several postdoctoral stays abroad, and a Marie Skłodowska-Curie Postdoctoral Fellowship (MSCA) facilitated his return. A young Ukrainian colleague also found employment with us via a similar MSCA grant for Ukrainian scientists. A year ago, in cooperation with the Institute of Organic Chemistry and Biochemistry of the CAS (Academy of Sciences of the Czech Republic; IOCB), we managed to recruit a married couple of chemists who had previously been at other top research groups. In Prague, they both got the opportunity to start their own independent careers, Dr. Gonsales at UCT Prague and her husband at IOCB. Working together as institutions, we try to provide them with excellent research facilities. Last but not least, I am pleased with the current cohort of young researchers who are slowly evolving from their junior status and are starting to succeed in getting their own grant-funded projects. The situation is therefore developing more optimistically than I had initially thought was possible.</p>


That some plastic ends up in incinerators? Fine with me.

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RECETOX (Research Centre for Toxic Compounds in the Environment) is an independent department of the Faculty of Science of Masaryk University in Brno, which has been established in 1983. RECETOX is focused on the research and education in cross-cutting area of Environment and Health. It addresses interactions among chemicals, environment, and biological systems, including consequences at local, regional, and global levels.

RECETOX - Centrum pro výzkum toxických látek v prostředí

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That some plastic ends up in incinerators? Fine with me.

Webinars LabRulezLCMS Week 32/2024

Insight into the molecular mechanisms of ALS

Introducing BIOCEV OMICS Mass Spectrometry Core Facility

In the next years, climate change will affect everything, says environmental epidemiologist Tomáš Janoš.

News from LabRulezLCMS Library - Week 30, 2024

Johns Hopkins Researchers Find Thousands of Unknown Chemicals in Electronic Cigarettes

Webinars LabRulezLCMS Week 31/2024

Nuclear Clocks and the Fundamental Constants of Nature

Atomic Nucleus Excited with Laser: A Breakthrough after Decades

Upcoming events

US HUPO 2026

Bruker at US HUPO 2026

Thermo Fisher Scientific at US HUPO 2026

Webinars

SCIEX OS software migration: Connect with the experts and ask your questions

Ion Pair HILIC-MS: A Powerful Characterization Method for Biomacromolecule Analysis

Cruise through genomics quantification and QC with Lunatic