<p><strong>Scientists at IOCB Prague are uncovering new details of gene transcription. They have identified a previously unknown molecular mechanism by which the transcription of genetic information from deoxyribonucleic acid (DNA) into ribonucleic acid (RNA) can be initiated. The researchers focused on a specific class of molecules known as alarmones, which are found in cells across a wide range of organisms and whose levels often increase under conditions of cellular stress. The results were published in the prestigious scientific journal </strong><i><strong>Nature Chemical Biology</strong></i><strong>.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_bc2bfffa6c.jpg" alt="IOCB Prague/Tomáš Belloň: Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription: Dr. Hana Cahová, head of the Chemical Biology of Nucleic Acids research group." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_bc2bfffa6c.jpg 234w," sizes="100vw" width="2000" height="1335"></p><div><p>Molecules of ribonucleic acid can carry a variety of chemical modifications at one end, known as caps. In eukaryotic organisms, including human cells, the best-known cap plays an important role in RNA stability and in regulating its subsequent fate. In recent years, however, it has become clear that alternative, non-canonical RNA caps also exist, although their formation and the mechanisms by which they are attached to RNA remain only partially understood. These include alarmone caps, formed by dinucleoside polyphosphate molecules, that protect cellular RNA at moments when the cell is under threat.</p><p>In their study,<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://cahova.group.uochb.cz/en"><strong>Dr. Hana Cahová</strong></a> and colleagues examined bacterial RNA polymerase and investigated how this enzyme can initiate transcription using dinucleoside polyphosphates (NpNs) instead of the standard RNA building blocks. For the first time, the scientists described, at the atomic level, how RNA bearing an alarmone cap can be generated directly at the initiation of gene transcription. They also observed that NpNs bind through a different type of base pairing than is typically observed.</p><p>The work was significantly shaped by <strong>Valentina Serianni from Hana Cahová’s team</strong>, who demonstrated the ability of dinucleoside polyphosphates to initiate gene transcription, and by <strong>Jana Škerlová</strong>, who focused on the structural analysis of RNA polymerase. Using cryogenic electron microscopy data, she showed how dinucleoside polyphosphate molecules bind within the active site of RNA polymerase – that is, the core of the enzyme where genetic information is transcribed. Together, their findings help to elucidate the processes that accompany the transcription of genetic information from DNA to RNA.</p><p>Hana Cahová adds: <i>“We’re describing something that truly occurs in cells and that we’re now able to observe directly at the level of individual molecules. This allows us to answer fundamental questions about cellular processes, such as how cells adapt to stress. RNA plays a central role in this, as it carries the cascade of information underlying any cellular response – for example, to threatening conditions caused by nutrient deprivation or temperature shock.”</i></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_2_0fe88ff9e9.jpg" alt="IOCB Prague/Tomáš Belloň: Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription: Dr. Tomáš Kouba, head of the Cryogenic Electron Microscopy core facility." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_2_0fe88ff9e9.jpg 234w," sizes="100vw" width="2000" height="1335"></p><div><p>Cryogenic electron microscopy (cryo-EM) was central to the project. This part of the work was led by<strong> Dr. Tomáš Kouba</strong>, one of the authors of the study. <i>“Cryogenic electron microscopy allows us to freeze biological molecules in a state very close to their natural form and then determine their three-dimensional structure. This makes it possible to look directly into the active centers of enzymes and observe their function down to the atomic level,”</i> he explains.</p><p>Last year, IOCB Prague opened a new <a target="_blank" rel="noopener noreferrer" href="https://cryoem.group.uochb.cz/en"><strong>cryo-EM center</strong></a><strong> </strong>that is unique within the Czech research environment. State-of-the-art cryogenic electron microscopes are housed in a specially designed building and enable the study of biological processes with exceptional structural precision.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_3_4d881e7a58.jpg" alt="IOCB Prague: Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription: This work shows how NpnNs initiate bacterial transcription. Cryo-EM reveals how nucleobases pair with the template: one in canonical and one in reverse Watson–Crick mode, providing a structural basis for their function as non-canonical RNA caps." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_3_4d881e7a58.jpg 245w," sizes="100vw" width="2000" height="1077"></p><blockquote><h4><strong>The Original article</strong></h4><h4><a target="_blank" rel="noopener noreferrer" href="https://www.nature.com/articles/s41589-025-02134-5"><strong>Molecular insight into 5′ RNA capping with Np<sub>n</sub>Ns by bacterial RNA polymerase</strong></a></h4><p>Valentina M. Serianni, Jana Škerlová, Anna Knopp Dubánková, Anton Škríba, Hana Šváchová, Tereza Vučková, Anatolij Filimoněnko, Milan Fábry, Pavlína Řezáčová, Tomáš Kouba &amp; Hana Cahova&nbsp;</p><p>Nat. Chem. Biol. 21 (2026)</p><p><a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1038/s41589-025-02134-5">https://doi.org/10.1038/s41589-025-02134-5</a></p><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6></blockquote><h4><strong>Abstract</strong></h4><p>RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from <i>Thermus</i> <i>thermophilus</i>. We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson–Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson–Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription.</p></div></div>

Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription

<p><strong>Food adulteration is a phenomenon with a long history that has gained increasing importance in recent years due to the globalization of food supply chains and strong economic pressures. Whether it involves diluting olive oil with cheaper oils, adding sugar to honey, or the hidden use of substitutes in protein supplements, the result is a loss of consumer trust and, in some cases, a potential risk to health. Analytical chemistry plays a key role in this area by providing methods and technologies capable of identifying and quantifying target compounds as well as unwanted impurities in a wide range of food matrices.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Watrex_Praha_Falsovani_potravin_a_jak_ho_odhali_analyticka_chemie_6912db5492.jpg" alt="Watrex: Food Adulteration and How It Is Revealed by Analytical Chemistry" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Watrex_Praha_Falsovani_potravin_a_jak_ho_odhali_analyticka_chemie_6912db5492.jpg 245w," sizes="100vw" width="1600" height="900"></p><h4><strong>The Role of Chromatography in Forensic Food Analysis</strong></h4><p>Chromatography, particularly liquid chromatography (HPLC), is one of the most effective analytical tools for separating complex mixtures of molecules. It enables:</p><ul><li>qualitative identification of individual components in a sample,</li><li>quantitative determination of their concentrations,</li><li>detection of impurities and unexpected components that may indicate<br>adulteration.</li></ul><p>In practice, HPLC is often combined with various types of detectors (UV/VIS, DAD, refractive index detectors) or with other techniques (e.g., mass spectrometry) to increase selectivity and sensitivity.</p><h4><strong>Isocratic vs. Gradient Elution</strong></h4><p>In the analysis of food samples, chromatographic methods are selected according to the analytical goal:</p><ul><li><strong>Isocratic HPLC </strong>uses a constant mobile phase composition throughout the analysis. It is simple, robust, and ideal for routine determinations of well-defined target analytes (e.g., sugars or vitamins).</li><li><strong>Gradient HPLC</strong> changes the mobile phase composition during separation, enabling better resolution of complex mixtures with a wide range of polarities (e.g., peptides or phenolic compounds).</li></ul><p>Gradient methods are particularly useful when analytes have very different properties and high separation efficiency is required.</p><h4><strong>Watrex Praha and the Contribution of Modern Systems to Food Analysis</strong></h4><p><a target="_blank" rel="noopener noreferrer" href="https://watrex.com/?utm_source=labrulez&amp;utm_medium=propagace&amp;utm_campaign=labrulez_clanky_HPLCsystemy"><strong>Watrex Praha, s.r.o.</strong></a> is one of the leading Czech manufacturers and distributors of liquid chromatography systems and instruments, with a long tradition dating back to 1990. The company has successfully transformed from a distributor into a manufacturer of its own HPLC and related technologies, focusing on modular, robust systems suitable even for demanding analytical tasks.</p><p>Their <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?manufacturerItems=93&amp;search=streamline"><strong>Streamline™ product line</strong></a><strong> </strong>includes several HPLC system concepts suitable for food analysis:</p><ul><li><strong>Isocratic HPLC system</strong> – a simple yet precise configuration with a single pump, column thermostat, and UV/VIS detector; suitable for routine determination of known analytes (e.g., basic carbohydrates, food additives).</li><li><strong>Binary gradient HPLC system</strong> – equipped with two pumps enabling mobile phase gradient formation, which enhances separation performance for complex mixtures<br>(e.g., phenolic profiles of wine, components of aromatic extracts).</li><li><strong>GPC/SEC system (Gel Permeation / Size Exclusion Chromatography)</strong> – a specialized solution for the determination of macromolecules and polymers, also relevant for the analysis of high-molecular-weight components in foods (e.g., polysaccharides).</li></ul><blockquote><p class="cke-user_style-important"><strong>👉</strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/Watrex_catalog_2024_ba97395f92.pdf"><strong>Product catalogue HERE</strong></a></p></blockquote><p>Thanks to the modular nature of these systems, analysts can easily adapt the configuration to a specific analytical problem, from simple routine analyses to complex characterization of food samples.</p><h4><strong>Practical Examples of Adulteration Revealed by HPLC</strong></h4><ul><li><strong>Detection of olive oil dilution: </strong>HPLC can separate and quantify characteristic triacylglycerols and fatty acids; unusual patterns indicate the presence of cheaper oils.</li><li><strong>Estimation of sugar addition in honey:</strong> Isocratic HPLC with a refractive index detector can determine sugar profiles (glucose, fructose, sucrose), revealing dilution or the addition of sugar syrups.</li><li><strong>Identification of aromatic adulterants in wine:</strong> Gradient HPLC with a PDA detector can reveal phenolic and aromatic profiles that are altered by the addition of synthetic compounds.</li></ul><h4><strong>Conclusion</strong></h4><p>Food adulteration remains a current issue that requires reliable and sensitive analytical methods. Liquid chromatography, and in particular modern HPLC systems, represent one of the most powerful tools for detecting unwanted additives, impurities, and unexpected components in complex food samples. Manufacturers such as <a target="_blank" rel="noopener noreferrer" href="https://watrex.com/?utm_source=labrulez&amp;utm_medium=propagace&amp;utm_campaign=labrulez_clanky_HPLCsystemy"><strong>Watrex Praha</strong></a> provide flexible chromatographic platforms covering a wide range of analytical tasks from simple isocratic to advanced gradient and GPC/SEC applications thereby supporting analysts in ensuring food quality and consumer protection.</p><blockquote><p>Did you find this article interesting? Follow <a target="_blank" rel="noopener noreferrer" href="https://watrex.com/?utm_source=labrulez&amp;utm_medium=propagace&amp;utm_campaign=labrulez_clanky_HPLCsystemy"><strong>Watrex Praha</strong></a> on their social media (<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/company/watrex/?viewAsMember=true"><strong>LinkedIn</strong></a> and <a target="_blank" rel="noopener noreferrer" href="https://www.facebook.com/WatrexPrague"><strong>Facebook</strong></a>) for more engaging topics.</p></blockquote>

Food Adulteration and How It Is Revealed by Analytical Chemistry

<p><strong>Join us for a fascinating conversation with Dr. Subhoja Chakraborty from the University of Central Florida, whose cutting-edge research targets the global challenge of malaria drug resistance. Dr. Chakraborty shares her journey from structure-based drug design during her PhD to her recent collaborative work repurposing human kinase inhibitors as rapid, selective antimalarials against drug-resistant Plasmodium falciparum strains.</strong></p><h4><strong>In this episode, you'll learn:</strong></h4><ul><li>How structure-guided approaches reveal potential drug targets, including cysteine proteases like falcipain-2, and kinases implicated in malaria's complex life cycle.</li><li>The power of repurposing kinase inhibitors originally developed for cancer and other diseases, focusing on compound 12, which blocks hemozoin formation and protein kinase 6—key steps in parasite survival.</li><li>Lab techniques such as affinity, gel filtration, and size exclusion chromatography for recombinant protein purification—and how troubleshooting is crucial for high-yield, stable complexes.</li><li>Advances in mass spectrometry for characterizing protein interactions, validating drug targets, and mapping molecular pathways pivotal to malaria therapeutics.</li><li>Tips and lessons for new researchers facing the challenges of sample preparation, complex protocols, and working as part of a collaborative team.</li></ul><p>Dr. Chakraborty’s insights bridge the gap between basic science and translational drug discovery, offering hope for more effective, targeted malaria treatments in a world where resistance to frontline therapies threatens millions.</p><h4><strong>Referenced Papers:</strong></h4><ul><li>"Plasmodium falciparum protein kinase 6 and hemozoin formation are inhibited by a type II human kinase inhibitor exhibiting antimalarial activity" (Cell Chemical Biology, 2025)</li><li>"New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain" (BBRC, 2022)</li><li>"Structure-Based Optimization of Protease−Inhibitor Interactions to Enhance Specificity of Human Stefin‑A against Falcipain‑2 from the Plasmodium falciparum 3D7 Strain" (Biochemistry, 2023)</li></ul><p>If you’re a student, scientist, or simply passionate about advances in infectious disease research, this episode offers actionable insights, inspiring advice, and a front-row seat to innovation in combating malaria.</p><h3><strong>Video Transcription</strong></h3><h4><strong>From Structural Biology to Drug Discovery: Chromatography and Mass Spectrometry in Malaria Research</strong></h4><h5><strong>Introduction</strong></h5><p>In this discussion, Subhoja shares insights into her research journey, focusing on malaria drug discovery and the role of modern analytical techniques in biological and biomedical research. The conversation is aimed primarily at undergraduate students and early-career researchers interested in chemistry, biotechnology, and life sciences.</p><h5><strong>Research Focus: Malaria Drug Discovery and Kinase Targets</strong></h5><p>Subhoja is currently involved in malaria drug discovery research at the University of Central Florida, where she has been working since beginning her postdoctoral position two years ago. Her earlier PhD research focused on structure-based drug design in malaria, using a combination of in silico approaches, recombinant protein expression, and X-ray crystallography to determine precise three-dimensional structures of target proteins and their inhibitors.</p><p>This structural perspective provided a foundation for her current work, which centers on drug discovery through compound screening and repurposing. A recent publication from her laboratory explores the use of repurposed mammalian CDK-like kinase inhibitors as potential antimalarial agents. While such kinase inhibitors are well known in cancer and cardiovascular research, their application to malaria targets represents a novel and promising approach.</p><p>Kinases are attractive drug targets because of their central role in cell signaling and growth pathways. By targeting specific kinases involved in different stages of the malaria parasite life cycle—whether asexual growth, gametocytogenesis, or differentiation—it may be possible to significantly inhibit parasite growth and progression.</p><h5><strong>Chromatography in Protein Expression and Purification Workflows</strong></h5><p>Chromatography plays a critical role throughout Subhoja’s research. Her experience spans from basic chromatography techniques during her early training to advanced protein purification workflows using affinity chromatography, gel filtration (size exclusion chromatography), and ion exchange chromatography.</p><p>Recombinant proteins are routinely purified using affinity resins such as nickel or cobalt, followed by further purification to remove contaminants. Fast Protein Liquid Chromatography (FPLC) enables compact, stepwise purification workflows suitable for producing proteins for in vitro assays.</p><p>A recurring challenge in this process is the expression of high-molecular-weight proteins, which often accumulate in insoluble fractions or inclusion bodies. Careful selection of expression vectors, host systems, and induction conditions is therefore essential to maximize yield and solubility.</p><h5><strong>Integrating Size Exclusion Chromatography into the Workflow</strong></h5><p>Size exclusion chromatography (SEC) is typically used after affinity purification to further improve protein purity. Following elution with imidazole or glutathione, desalting is required to prevent buffer components from interfering with downstream assays. This is often achieved using desalting columns such as G-25 or PD-10.</p><p>To remove lower-molecular-weight contaminants, finer SEC media—such as Superdex or Sephacryl columns—are employed. Concentration steps using molecular-weight cut-off filters are then applied to obtain the desired protein concentration for functional studies.</p><p>These iterative purification and troubleshooting steps are a routine part of protein biochemistry and reflect the importance of methodical optimization and careful validation.</p><h5><strong>The Role of Mass Spectrometry in Biomolecular Characterization</strong></h5><p>Mass spectrometry is a key analytical tool in Subhoja’s research pipeline, particularly for target identification and validation. In both malaria and cancer research, MS is used alongside chromatography, immunoprecipitation, and pull-down assays to study protein interactions and molecular recognition events.</p><p>Affinity-based mass spectrometry enables the identification of binding partners and interactors, whether studying proteins, long non-coding RNAs, or protein complexes. Techniques such as native MS, tandem affinity purification, and proximity labeling (e.g., TurboID-based workflows) provide deeper insights into molecular networks and signaling pathways.</p><p>These approaches are essential for understanding how candidate drug targets function within complex biological systems.</p><h5><strong>Sample Preparation Challenges in Biological Research</strong></h5><p>Sample preparation remains one of the most challenging aspects of biological experimentation. Whole-cell lysates contain proteases, nucleases, and other components that can rapidly degrade target molecules. Preventing degradation requires minimizing preparation time, maintaining low temperatures, and using appropriate inhibitor cocktails.</p><p>Reproducibility is also critical: biological experiments require multiple replicates, and variability is often unavoidable. Careful handling, protocol optimization, and continuous troubleshooting are essential to ensure reliable results, whether preparing samples for chromatography, mass spectrometry, sequencing, or immunoprecipitation.</p><h5><strong>Advances in Chromatography and MS for Malaria Research</strong></h5><p>Modern advances in chromatography and mass spectrometry significantly enhance malaria research by enabling precise target identification, quantification, and functional characterization. Drug discovery workflows begin with construct design and recombinant expression, followed by purification and interaction studies.</p><p>In malaria research, stage-specific parasite biology requires careful extraction and analysis of proteins from different life cycle stages. Tandem affinity MS, immunoprecipitation, and in vivo validation studies help confirm target relevance and therapeutic potential.</p><p>Recent work on repurposed kinase inhibitors has shown promising results, including inhibition of hemozoin formation—a key detoxification pathway for the malaria parasite—highlighting the potential of such compounds for further development.</p><h5><strong>Malaria, Drug Resistance, and Global Impact</strong></h5><p>Malaria remains a major global health burden, with over 600,000 deaths annually and widespread drug resistance complicating treatment. Artemisinin resistance, particularly associated with mutations in the K13 propeller domain, has driven the search for new targets and therapies.</p><p>During her PhD, Subhoja focused on falcipain-2, a cysteine protease involved in hemoglobin degradation within the parasite. This pathway is critical for parasite survival and has emerged as a promising drug target. Her work revealed that falcipain-2 operates within a larger protein complex responsible for hemoglobin processing and amino acid release.</p><p>Understanding these molecular mechanisms is essential for developing robust, stage-specific antimalarial strategies.</p><h5><strong>Advice for Early-Career Researchers</strong></h5><p>For researchers just starting out, Subhoja emphasizes the importance of hands-on experience. Working directly with cells, lysates, and analytical tools is essential for truly understanding experimental systems. Failure is an inherent part of research, and perseverance is key.</p><p>Motivation, teamwork, careful sample handling, and thorough preparation all contribute to long-term success. Reading extensively, critically evaluating one’s own work, and appreciating incremental progress are vital aspects of a sustainable research career.</p><p>Every successful experiment—no matter how small—represents meaningful progress and contributes to the broader goals of science and medicine.</p><h5><strong>Closing Remarks</strong></h5><p>The discussion highlights how interdisciplinary approaches combining chromatography, mass spectrometry, structural biology, and biochemistry are driving advances in malaria drug discovery. Through careful experimental design, analytical rigor, and collaborative teamwork, researchers can address complex biological challenges and contribute to global health solutions.</p><blockquote><p><strong>This text has been automatically transcribed from a video presentation using AI technology. It may contain inaccuracies and is not guaranteed to be 100% correct.</strong></p></blockquote><blockquote><h4><strong>Concentrating on Chromatography Podcast</strong></h4><p>Dive into the frontiers of chromatography, mass spectrometry, and sample preparation with host David Oliva. Each episode features candid conversations with leading researchers, industry innovators, and passionate scientists who are shaping the future of analytical chemistry. From decoding PFAS detection challenges to exploring the latest in AI-assisted liquid chromatography, this show uncovers practical workflows, sustainability breakthroughs, and the real-world impact of separation science. Whether you’re a chromatographer, lab professional, or researcher you'll discover inspiring content!</p><p>You can find <strong>Concentrating on Chromatography Podcast </strong>in podcast apps:</p><ul><li><a target="_blank" rel="noopener noreferrer" href="https://open.spotify.com/show/1wZg67rCjoGju4yhqxI3tL"><strong>Spotify</strong></a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podcasts.apple.com/tz/podcast/concentrating-on-chromatography/id1788429185"><strong>Apple podcast</strong></a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podscan.fm/podcasts/concentrating-on-chromatography"><strong>podscan</strong></a></li></ul><p>and on <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@ChromatographyTalk/videos"><strong>YouTube channel</strong></a></p></blockquote>

Affinity, Gel Filtration, Size Exclusion Chromatography: Repurposing Kinase Inhibitors for Malaria

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Food

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Science and research

The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) is a leading scientific institution in the Czech Republic, recognized internationally. Its primary mission is basic research in the fields of chemical biology and medicinal chemistry, organic and material oriented chemistry, chemistry of natural compounds, biochemistry and molecular biology, physical chemistry, theoretical chemistry, and analytical chemistry. 

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

Organomation, founded in 1959, designs and manufactures high-quality nitrogen evaporators and extraction systems. Known for innovation and durability, their lab instruments are used globally for efficient sample preparation with strong customer support.

Organomation

WATREX Prague is the distributor and producer of HPLC techniques in the Czech Republic and Slovakia. Main Chromatografic and Related Techniques Supported: LC, GPC, IC, IEC, Automated SPE, LC Columns and special column packings, LC method development, Software development, Laboratory Robots.

Watrex Praha

Waters Xevo MRT QTof Mass Spectrometer

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Maximum performance, matched to throughput levels that matter for complex and challenging analyses, increases statistical power and confidence in results.</p><h5><strong>Feeling trapped?</strong></h5><p>Unlike other high-resolution MS technologies, multi-reflecting time-of-flight delivers mass resolution consistent over a broad m/z range independent of scan speed, even at the fastest acquisition rates for MS and MS/MS data, ensuring confident identification of analytes across a range of samples and matrices – an ideal solution for metabolite profiling and discovery.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_MRT_Mass_Spectrometer_Extraordinary_Performance_d8879eda23.jpg" alt="Waters Xevo MRT Mass Spectrometer: Extraordinary Performance." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_MRT_Mass_Spectrometer_Extraordinary_Performance_d8879eda23.jpg 245w," sizes="100vw" width="1309" height="774"></p><h3><strong>Connected Solutions</strong></h3><h4><strong>From advanced chemistry to flexible informatics</strong></h4><p>Make meaningful scientific discoveries more efficient with dedicated workflows combining column chemistries, separations, and informatics with the exceptional data quality of the Xevo MRT Mass Spectrometer. The waters_connect™ platform allows you to process and report your data in the way that you want. Whether using a Waters supported solution or exporting data via mzML to custom scripted workflows, we have you covered.</p><h4><strong>The Xevo MRT mass spectrometer readily integrates with your existing pipeline and workflow strategy</strong></h4><p>Waters has partnered with Mass Analytica™ (mass-analytica.com) and their market leading metabolomic, lipidomic, and metabolite identification software packages, MARS, Lipostar2, and MassMetaSite, respectively. Through either the waters_connect Application Programming Interface (API) or via mzML*, there is the option for you to transfer your data into the relevant software package for statistical interpretation and identification of analytes.</p><p>The DATA Convert Application within the waters_connect Platform enables you to convert to and export mzML file formats, ensuring a seamless integration of technology and informatics for every lab.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_MRT_Hmotnostni_spektrometr_6_d0fc257136.jpg" alt="Waters Xevo MRT Mass Spectrometer: Connected Solutions." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_MRT_Hmotnostni_spektrometr_6_d0fc257136.jpg 236w," sizes="100vw" width="1212" height="802"></p><p>The waters_connect platform provides flexible data processing options, either using third-party applications via the waters_connect API or conversion of data sets to mzML file format via DATA Convert.&nbsp;</p><h3><strong>Unlocking a New Level of Confidence&nbsp;</strong></h3><h4><strong>By bringing an analytical powerhouse to every lab</strong>&nbsp;</h4><p>To meet the most challenging analytical problems that you experience head on, Waters has taken cutting edge technology that was pioneered in the SELECT SERIES™ MRT, scaling the raw power and resolution at speed into a compact flexible, benchtop platform.</p><h4><strong>The MRT Xevolution</strong></h4><p>The Xevo MRT Mass Spectrometer has been engineered to deliver high-end technology into a benchtop platform to solve your most challenging problems. The novel acquisition system, with dual gain analogue-to-digital converter, delivers long term system stability over a high dynamic range, ensuring exceptional quality data with consistent robustness and reproducibility.</p><p>The 4 m flight path with a total of 8 reflections within the MRT mass analyzer, achieves 100,000 FWHM resolution at scan rates of up to 100 Hz - for ultimate MS/MS performance.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_MRT_Hmotnostni_spektrometr_Schema_2448b0bc8d.jpg" alt="Waters Xevo MRT Mass Spectrometer: The Xevo MRT Mass Spectrometer schematic. ​" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_MRT_Hmotnostni_spektrometr_Schema_2448b0bc8d.jpg 236w," sizes="100vw" width="1199" height="794"></p>

Quantitative analysis of proteins (Bioanalytic) 

In our laboratory, proteomic analyses, including quantitative analysis of proteins, are performed by HPLC-MS or HPLC-MS/MS methods on a ZenoTOF 7600 high-resolution mass spectrometer (SCIEX).

<p><strong>Quantitative analysis of proteins is important in many industries and applications. Proteins include a diverse group of compounds that participate in virtually every biological process. Proteins are building blocks, hormones, transport molecules, cell receptors, cell growth and differentiation factors. Because of this, the analysis of protein interactions is crucial in drug design and production.</strong></p><p>Proteins are macromolecules - the basis of their structure are polypeptide chains containing from 100 to more than 10000 amino acids (10 - 100 kDa). Proteins are found in simple and complex forms. Complex proteins contain a non-protein component (sugar, lipids, metal ions or dyes) in their structure.</p><p>In our laboratory, proteomic analyses, including quantitative analysis of proteins, are performed by HPLC-MS or HPLC-MS/MS methods on a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?manufacturerItems=52&amp;search=ZenoTOF+7600"><strong>ZenoTOF 7600</strong></a> high-resolution mass spectrometer (SCIEX). We process the obtained results using Sciex OS, Spectronaut, Skyline software.</p><h4><strong>MS vs MS/MS</strong></h4><p>Quantitative analysis of intact protein (whole protein in intact form) leads to the concentration (determined from a prepared curve from a standard (with or without matrix) and confirmation of the identification by superimposing (on a mirrored basis) the MS spectrum of the protein determined in the sample to the MS spectrum of the standard. For your needs, we can generate a list of protein-structured compounds (impurities) that were identified in the sample and determine the ratio of their signal area to the signal area of the analyzed protein.</p><p>The result of proteomic quantitative peptide analysis allows precise and much more sensitive determination of protein concentration. The analysis is based on MS/MS data obtained for peptides obtained by digestion with proteolytic enzymes. The reported result consists of the concentration of the protein under study and confirmation of its presence based on the determined amino acid sequence. For such analyses, it is recommended to add standards internal standards.</p><blockquote><p><span style="font-size:22px;"><strong>Our offer:</strong></span></p><ul><li>For proteins and peptides with low masses - intact analysis with MS detection;</li><li>Proteins with masses &gt;20kDa require optimization of the digestion method and MS/MS detection. This results in specific signals from the analyzed protein in the mixture/matrix;</li><li>From complex matrices (including serum, cell culture, fungal suspension), sample analysis involves several steps:&nbsp;<ul><li>Sample purification;</li><li>Digestion to obtain unique peptides to distinguish the analyzed proteins from other proteins in the sample;</li><li>Sample preparation requires appropriate method optimization and validation (let's set validation criteria individually);</li></ul></li><li>Reported quantitative result includes confirmation of the presence of the protein in native form or a peptide derived from it (usually confirmation includes at least two peptide sequences);</li><li>Statistical analysis using tools: MarkerView (PCA), GraphPad Prism, Trends, Sciex OS.</li></ul><p><i>To optimize and validate the method, it is necessary to provide a standard, in the case of proteins with high masses - it is recommended to add an internal standard.</i></p><p>See also:</p><ul><li><a target="_blank" rel="noopener noreferrer" href="https://labexperts.com.pl/service/identyfikacja-bialek/"><strong>Protein identification</strong></a><strong>,</strong></li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1296"><strong>Analysis and characterization of monoclonal antibodies</strong></a><strong>.</strong></li></ul></blockquote><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Bioanalytic_Bioanalytic_Quantitative_analysis_of_proteins_1_de494646f2.jpg" alt="Bioanalytic: Quantitative analysis of proteins." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Bioanalytic_Bioanalytic_Quantitative_analysis_of_proteins_1_de494646f2.jpg 200w," sizes="100vw" width="777" height="606"></p>

Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry

The Xevo® G2-XS QTof combines StepWaveTM ion optics with the XS Collision Cell, providing a significant increase in sensitivity with no reduction in selectivity.

<h4><strong>eXtreme Sensitivity, eXtraordinary Selectivity, eXceptional Solutions</strong></h4><div><p><strong>For the scientist who needs to identify, quantify and confirm the broadest range of compounds in the most complex and challenging samples.</strong></p><ul><li>Maximum robustness with no compromise in performance</li><li>Class-leading real-world quantitative sensitivity</li><li>Highest quality, most comprehensive qualitative information</li><li>Flexibility to adapt to changing needs</li><li>Accessible to experts and non-experts alike</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_1_b9f8dd32be/Waters-Xevo-G2-XS-QTof-Quadrupole-Time-of-Flight-Mass-Spectrometry-1.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_1_b9f8dd32be/thumbnail_Waters-Xevo-G2-XS-QTof-Quadrupole-Time-of-Flight-Mass-Spectrometry-1.jpg 173w," sizes="100vw" width="1099" height="991"></p><h3><strong>Overview</strong></h3><div><h4><strong>Maximum robustness with no compromise in performance</strong></h4><p>The trend for increasing complexity of both samples and studies can result in difficulty obtaining high quality data for every component of interest while maintaining optimum performance throughout the analysis.</p><p>The <strong>Xevo® G2-XS QTof</strong> combines <strong>StepWave<sup>TM</sup> ion optics</strong> with the <strong>XS Collision Cell</strong>, providing a significant increase in sensitivity with no reduction in selectivity.&nbsp; During long analyses, critical hardware components stay clean for longer, so results are more reproducible and the laboratory stays productive.</p><p>Meaningful information is obtained for a greater number of components across a larger population of samples than ever before, giving a more complete picture for improved understanding and more confident decision making.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_437f84bacd.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry: Maximum robustness with no compromise in performance." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_437f84bacd.jpg 224w," sizes="100vw" width="900" height="628"></p><div><h4><strong>Class-leading real-world quantitative sensitivity</strong></h4><p>In targeted quantitative analysis, the greatest challenge is to detect and quantify components of interest down to the lowest possible levels, often in the presence of interferences from complex matrix.&nbsp; Large variation in the concentrations of different components further adds to this challenge.</p><p>The <strong>Xevo G2-XS QTof</strong> combines sensitivity and selectivity with the mass accuracy, dynamic range and speed provided by <strong>QuanTofTM technology</strong> and the enhanced quantitative capability of <strong>Tof-MRM data acquisition</strong>.&nbsp; The end result is class-leading quantitative performance in real everyday laboratory conditions, demonstrated by limits of detection and quantification superior to anything achieved before with high resolution MS.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_2_d805c7aa49.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry: Class-leading real-world quantitative sensitivity." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_2_d805c7aa49.jpg 245w," sizes="100vw" width="900" height="312"></p><div><h4><strong>Highest quality, most comprehensive qualitative information</strong></h4><p>In addition to accurate quantitative profiles, complete understanding of a sample requires detailed and comprehensive qualitative information.</p><p><strong>MS<sup>E</sup></strong> is a simple but powerful approach that delivers accurate mass precursor and fragment ion data for every detectable component, whether chromatographically resolved or not.&nbsp; This represents the ultimate in qualitative information, and because the approach is un-targeted, the data can be interrogated again later as scientific questions evolve.</p><p><strong>FastDDA</strong> is an automated, targeted data acquisition method that provides rapid, intelligent accurate mass MS/MS capability for confirmation of known compounds or characterization of unknowns, for situations where only true MS/MS data will suffice.</p><h4><strong>Flexibility to adapt to changing needs</strong></h4><div><p>The growing emphasis on efficiency and productivity in the laboratory demands analytical systems that are not only robust and reliable, but that also have the flexibility to accomplish a wide variety of tasks today, with future-proofing for the innovations of tomorrow.&nbsp;</p><p><strong>Waters’ Universal Ion Source Architecture</strong> enables the use of a single analytical platform for many different applications and molecule types, as well as providing the option to add new functionality as requirements and priorities change.&nbsp; All source options are designed to be quickly interchangeable and ready to use within minutes, maximizing versatility and minimizing downtime.</p><div><h3><strong>Accessible to experts and non-experts alike</strong></h3><p>Traditionally the ability to achieve and maintain optimum performance from such a powerful analytical system would require a level of knowledge and experience held only by expert users.</p><p>The <strong>Xevo G2-XS QTof</strong> features <strong>IntelliStartTM technology</strong>, an intuitive user interface that automates routine tasks and ensures reproducible data of the highest quality, ensuring the full capability of the system is accessible to all.</p><p><strong>IntelliStart enables essential functions to be carried out automatically:</strong></p><ul><li>MS resolution and calibration checks</li><li>Simple setup of diverse experiments</li><li>Scheduled LC-MS system checks</li><li>Continuous system monitoring</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_3_279cf35277.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry: Accessible to experts and non-experts alike." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_3_279cf35277.jpg 136w," sizes="100vw" width="900" height="1038"></p></div></div></div></div></div></div>

Products focused on LC/TOF - page 2

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