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 Nature Chemical Biology.<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"><div>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.In their study, <a target="_blank" rel="noopener noreferrer" href="https://cahova.group.uochb.cz/en">Dr. Hana Cahová</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.The work was significantly shaped by Valentina Serianni from Hana Cahová’s team, who demonstrated the ability of dinucleoside polyphosphates to initiate gene transcription, and by Jana Škerlová, 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.Hana Cahová adds: “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.”<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"><div>Cryogenic electron microscopy (cryo-EM) was central to the project. This part of the work was led by Dr. Tomáš Kouba, one of the authors of the study. “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,” he explains.Last year, IOCB Prague opened a new <a target="_blank" rel="noopener noreferrer" href="https://cryoem.group.uochb.cz/en">cryo-EM center</a> 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.<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"><blockquote><h4>The Original article</h4><h4><a target="_blank" rel="noopener noreferrer" href="https://www.nature.com/articles/s41589-025-02134-5">Molecular insight into 5′ RNA capping with NpnNs by bacterial RNA polymerase</a></h4>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;Nat. Chem. Biol. 21 (2026)<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><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a></h6></blockquote><h4>Abstract</h4>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 Thermus thermophilus. 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.</div></div>

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

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.<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"><h4>The Role of Chromatography in Forensic Food Analysis</h4>Chromatography, particularly liquid chromatography (HPLC), is one of the most effective analytical tools for separating complex mixtures of molecules. It enables:<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 adulteration.</li></ul>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.<h4>Isocratic vs. Gradient Elution</h4>In the analysis of food samples, chromatographic methods are selected according to the analytical goal:<ul><li>Isocratic HPLC 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>Gradient HPLC 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>Gradient methods are particularly useful when analytes have very different properties and high separation efficiency is required.<h4>Watrex Praha and the Contribution of Modern Systems to Food Analysis</h4><a target="_blank" rel="noopener noreferrer" href="https://watrex.com/?utm_source=labrulez&amp;utm_medium=propagace&amp;utm_campaign=labrulez_clanky_HPLCsystemy">Watrex Praha, s.r.o.</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.Their <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?manufacturerItems=93&amp;search=streamline">Streamline™ product line</a> includes several HPLC system concepts suitable for food analysis:<ul><li>Isocratic HPLC system – 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>Binary gradient HPLC system – equipped with two pumps enabling mobile phase gradient formation, which enhances separation performance for complex mixtures (e.g., phenolic profiles of wine, components of aromatic extracts).</li><li>GPC/SEC system (Gel Permeation / Size Exclusion Chromatography) – 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>👉<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/Watrex_catalog_2024_ba97395f92.pdf">Product catalogue HERE</a></blockquote>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.<h4>Practical Examples of Adulteration Revealed by HPLC</h4><ul><li>Detection of olive oil dilution: HPLC can separate and quantify characteristic triacylglycerols and fatty acids; unusual patterns indicate the presence of cheaper oils.</li><li>Estimation of sugar addition in honey: Isocratic HPLC with a refractive index detector can determine sugar profiles (glucose, fructose, sucrose), revealing dilution or the addition of sugar syrups.</li><li>Identification of aromatic adulterants in wine: Gradient HPLC with a PDA detector can reveal phenolic and aromatic profiles that are altered by the addition of synthetic compounds.</li></ul><h4>Conclusion</h4>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">Watrex Praha</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.<blockquote>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">Watrex Praha</a> on their social media (<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/company/watrex/?viewAsMember=true">LinkedIn</a> and <a target="_blank" rel="noopener noreferrer" href="https://www.facebook.com/WatrexPrague">Facebook</a>) for more engaging topics.</blockquote>

Food Adulteration and How It Is Revealed by Analytical Chemistry

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.<h4>In this episode, you'll learn:</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>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.<h4>Referenced Papers:</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>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.<h3>Video Transcription</h3><h4>From Structural Biology to Drug Discovery: Chromatography and Mass Spectrometry in Malaria Research</h4><h5>Introduction</h5>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.<h5>Research Focus: Malaria Drug Discovery and Kinase Targets</h5>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.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.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.<h5>Chromatography in Protein Expression and Purification Workflows</h5>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.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.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.<h5>Integrating Size Exclusion Chromatography into the Workflow</h5>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.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.These iterative purification and troubleshooting steps are a routine part of protein biochemistry and reflect the importance of methodical optimization and careful validation.<h5>The Role of Mass Spectrometry in Biomolecular Characterization</h5>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.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.These approaches are essential for understanding how candidate drug targets function within complex biological systems.<h5>Sample Preparation Challenges in Biological Research</h5>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.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.<h5>Advances in Chromatography and MS for Malaria Research</h5>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.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.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.<h5>Malaria, Drug Resistance, and Global Impact</h5>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.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.Understanding these molecular mechanisms is essential for developing robust, stage-specific antimalarial strategies.<h5>Advice for Early-Career Researchers</h5>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.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.Every successful experiment—no matter how small—represents meaningful progress and contributes to the broader goals of science and medicine.<h5>Closing Remarks</h5>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.<blockquote>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.</blockquote><blockquote><h4>Concentrating on Chromatography Podcast</h4>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!You can find Concentrating on Chromatography Podcast in podcast apps:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://open.spotify.com/show/1wZg67rCjoGju4yhqxI3tL">Spotify</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podcasts.apple.com/tz/podcast/concentrating-on-chromatography/id1788429185">Apple podcast</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podscan.fm/podcasts/concentrating-on-chromatography">podscan</a></li></ul>and on <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@ChromatographyTalk/videos">YouTube channel</a></blockquote>

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

Article

Product

Video

Scientists

Food

Interview

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

DataApex Clarity Offline Chromatography Software

Clarity Offline allows users to import previously acquired data and to evaluate and prepare methods in regulated environment.

Clarity Offline allows users to import previously acquired data and to evaluate and prepare methods. This version cannot acquire data, but it can share data or even directly access (through LAN) projects of the <a href="https://lcms.labrulez.com/products/999">Clarity</a> and Clarity Lite software. With Clarity Offline users are able to work with acquired data on additional computers in the lab or at home. The software works with the same files and provides the same outputs (printing and exporting) as Clarity and Clarity Lite.
Clarity Offline is intended for use as additional software that supplements Clarity and Clarity Lite. It can also be used to evaluate data from other manufacturers&#39; CDS.
<blockquote>
Ask for <a href="https://www.dataapex.com/product/clarity-demo">Clarity Demo version</a> which allows you to get your hands on software before purchase
</blockquote>
<h3>Main features</h3>
<ul>
<li>21 CFR Part 11 compliance: Clarity Offline contains all functions (Electronic Signatures, User Accounts, Audit Trail, etc.) for compliance with the 21 CFR Part 11 directive of the FDA. Clarity Offline can be used for evaluation in regulated environments.
</li>
<li>Networked Solution: Clarity Offline can access files of Clarity and Clarity Lite installed on networked computers. This enables evaluation of chromatograms, development of new methods, and printing reports on additional computers in the laboratory.
</li>
<li>Education: An additional field of use is in education. Students can process chromatograms that have been acquired from Clarity connected to a chromatograph using their Clarity Offline license. Thus they do not need a Clarity full license just for data evaluation.
</li>
<li>Data processing and evaluation from other chromatography software: Clarity Offline allows the import of data from other chromatography software using text or AIA import function. This allows the user to process and evaluate chromatograms acquired by other chromatography software.
</li>
<li>Offsite computer: Clarity Offline can be installed on any Windows computer, giving you anytime access to your chromatographic data (USB hardware key is required).
</li>
<li>Language Localizations available: Useful for non-English speakers. At the moment, there are French, German, Russian, Spanish, and Chinese localizations available in a single installation package. Simply switch to your preferred language anytime.
</li>
</ul>
<a href="https://www.dataapex.com/controls">List of supported instruments</a>
<a href="https://www.dataapex.com/product/clarity-std-compatibility">Compatible Windows OS and Hardware</a>
<a href="https://www.dataapex.com/product/clarity-21cfr-compliance">Clarity 21 CFR Part 11 compliance</a>

DataApex PDA - Photodiode Array Extension for Clarity

The PDA Extension is an optional Extension that is used for processing data that has been acquired from selected photo diode array detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis.

<h3>Extension for 3D data analysis from Photodiode Array Detectors</h3>
The PDA Extension is an optional Extension that is used for processing data that has been acquired from selected photo diode array detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis. This extension expands the capability of <a href="https://lcms.labrulez.com/products/999">Clarity</a> by providing interactive spectral analysis, peak purity analysis and compound identification that is based on a spectral library search. PDA data can be displayed in a set of optional views including 3D rendering.
All data is saved in a single file; a chromatogram at any wavelength or even only a spectrum can simply be recalled for review after an analysis. UV-VIS spectra, acquired using a PDA detector, may be interactively selected from a chromatogram signal for visual inspection and comparison. The spectra may also be used for peak purity determinations, wavelength optimization and component identification through spectral libraries.
<h4>Main features</h4>
<ul>
<li>PDA View: The PDA view is customizable; up to four views can be displayed at one time (Any combination from the following views may be selected: Isoplot, Chromatogram, Spectra, 3D Display, Peak Purity, Peak Purity Spectra, Library Spectra Search and Spectral Library). The user can easily extract chromatographic signals from PDA data to determine the optimal detection wavelength for each peak.
</li>
<li>PDA Method: The Clarity PDA method includes an option for Spectral Library Search and Peak Purity analysis.
</li>
<li>Limit values: These calculated values are compared to user-set limit values, either for each chromatogram separately or together for the selected series. Deviation of a certain parameter from the permissible limits is immediately reported and may lead to the termination of the sequence in progress.
</li>
<li>Spectral Library: The Clarity software compares the peak spectra with the spectra of an unlimited number of spectral libraries. Spectra stored in a Spectral Library include retention times and analysis parameters (optional). The Spectral Library Search can perform automatic identification of integrated/calibrated components (peaks). The library search may be constrained by the RT Window and by Wavelength Range. Either the Least Square, the Weighted Least Square or the Correlation Method is used for calculating library search matches. A Background Correction option is also available.
</li>
<li>Peak Purity: This analysis helps to discover hidden impurities. Peak Purity test is applied to all integrated/calibrated peaks in the active signal. Purity is calculated from 5 or all spectra within the peak. The similarity curve is displayed in the PDA window. Peak Purity analysis can be optimized by setting custom preferences relating to the purity threshold, wavelength restriction and absorbance threshold.
</li>
<li>Import/Export Data: Spectral data can be imported/exported in ASCII text formats to or from the <a href="https://lcms.labrulez.com/products/999">Clarity software</a>.
</li>
<li>Reports: Users can easily include PDA options such as data 3D Display, Isoplot, Spectra, Peak Purity and Library Search results in reports using the intuitive Report Setup Dialog.
</li>
<li>Instrument Control: Control modules for Agilent 1100 DAD and FLD, Sykam S3210/3240, Knauer PDA and many others are available. Additional control modules for other PDA detectors can be developed upon request.
</li>
</ul>
<a href="https://www.dataapex.com/controls#9709a8ca9130f20fc18c284302efd33b">List of controlled PDA detectors</a>

DataApex SST - System Suitability Test Extension for Clarity

The SST extension serves to monitor the correct function of the chromatography system. The program compares up to 12 selected parameters (e.g., retention time, efficiency, asymmetry of peaks) calculated according to one of three pre-selected methods (USP, EP, JP).

<h3>The SST extension serves to monitor the correct function of the chromatography system.</h3>
The program compares up to 12 selected parameters (e.g., retention time, efficiency, asymmetry of peaks) calculated according to one of three pre-selected methods (USP, EP, JP). These calculated values are either compared to the user&#39;s set limit values for each chromatogram separately or together for the selected series. Deviation of any parameter from the permissible limits is immediately reported and may lead to the termination of the sequence in progress. The SST Extension allows the user to monitor the parameters of individual substances and thus evaluate the reproducibility of the results of the entire chromatography system.
The SST extension is required when using the <a href="https://www.dataapex.com/product/validation-kit">Validation Kit</a>.
<h3>Main features</h3>
<ul>
<li>Measuring: Simultaneous data acquisition from up to four signals (detectors) attached to one chromatograph.
</li>
<li>Parameters: The program compares up to 12 selected parameters (e.g., retention time, efficiency, asymmetry of peaks) calculated according to one of three pre-selected methods (USP, EP, JP).
</li>
<li>Limit values: These calculated values are compared to user set limit values, either for each chromatogram separately or together for the selected series. Deviation of a certain parameter from the permissible limits is immediately reported and may lead to the termination of the sequence in progress.
</li>
<li>Versatility: Even though validation primarily focuses on testing system reliability, it can also be used in many other ways. Validation can be run during measurements, or additionally, using batch processing. Validated data can be automatically saved to a database file for further processing.
</li>
<li>Enhanced sequencing: In connection with a sequence, the SST module can even pause a sequence when a specified value has been exceeded or to perform predefined functions.
</li>
</ul>
<a href="https://gcms.labrulez.com/products/999">Clarity</a> Chromatography Software required

DataApex MS - Mass Spectrometry Extension for Clarity

The Clarity MS Extension is a tool that is used for processing data that has been acquired from selected Mass Spectrometry detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis.

<h3>Clarity Extension for processing data that has been acquired from selected Mass Spectrometry detectors</h3>
The Clarity MS Extension is a tool that is used for processing data that has been acquired from selected Mass Spectrometry detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis.
The MS Extension expands the capability of <a href="https://lcms.labrulez.com/products/999">Clarity</a> and <a href="https://lcms.labrulez.com/products/1000">Clarity Offline</a> Chromatography software by providing interactive spectral analysis, peak purity analysis, and compound identification that is based on a spectral <a href="https://gcms.labrulez.com/products?category=249">library</a> search. The extension is prepared to function with single quadrupole MS detectors and TOF MS detectors.
All data is saved in a single file; a chromatogram at any m/z value or even only a spectrum can simply be recalled for review after an analysis. MS spectra, acquired using an MS detector, may be interactively selected from a chromatogram signal for visual inspection and comparison. The spectra may also be used for peak purity determinations and component identification through spectral <a href="https://lcms.labrulez.com/products?category=285">libraries</a>.
It is possible to import MS data in AIA (cdf), mzXML, MzML, and mzData formats.
Control modules for selected detectors (see <a href="https://www.dataapex.com/controls">list of control modules</a>) are available in Clarity. Additional control modules for MS detectors can be developed upon request.

DataApex GPC - Gel Permeation Chromatography Extension for Clarity 

GPC Extension provides interactive and automated GPC analysis, including recalibration and GPC reporting, as well as simplifies the retrieval of GPC data. The GPC Extension allows flow rate and multi-detector delay corrections and includes Narrow, Broad, and Broad on Narrow calibrations.

<h3>Extension provides interactive and automated GPC analysis, including recalibration and GPC reporting, as well as simplifies the retrieval of GPC data.</h3>
Gel Permeation Chromatography (GPC) / Size Exclusion Chromatography (SEC) is the technique used for obtaining a rapid and reliable characterization of polymer molecular weight and molecular weight distribution. GPC Extension provides interactive and automated GPC analysis, including recalibration and GPC reporting, as well as simplifies the retrieval of GPC data. The GPC Extension allows flow rate and multi-detector delay corrections and includes Narrow, Broad, and Broad on Narrow calibrations.
<h3>Main features</h3>
<ul>
<li>Data Acquisition: Simultaneous data acquisition from up to four four-detector chromatographs (4×4 configuration), detector delay correction for multidetector measurement. 
</li>
<li>Data Processing: The same chromatograms can be evaluated in both standard and GPC modes. Multiple peaks and multiple signals are processed in one chromatogram.
</li>
<li>GPC Integration: Separate integration tables for GPC and standard evaluation are used. There are extensive possibilities for modifying chromatograms. The chromatogram integration can be changed by entering global parameters or interactively, through the direct graphical modification of the baseline.
</li>
<li>Calibration: Narrow, Broad, Broad on Narrow standard calibration methods combined with Flow Rate correction and Universal calibration. Manual calibration or automated recalibration from a sequence. Multiple Broad standards can be used.
</li>
<li>GPC Calculations: Polynomial (n= 1-5) curve fits (independent for signals), Mp, Mn, Mw, Mv, Mz, Mz+1 molecular weight averages and polydispersity.
</li>
<li>Graphs: Molecular weight distribution graphs. Overlay: Simultaneously displays a virtually unlimited number of chromatograms. Overlay of dW/d logM vs. log M and cumulative height graphs.
</li>
<li>Export: Slice Table results, graphs, result and summary tables.
</li>
<li>User Calculations: Users can define custom calculations in the Result and Summary tables. Using the integrated editor, you can create your own columns from the original columns and individual mathematical functions.
</li>
<li>GPC Results Table: Displays molecular weight averages together with peak details for active signal. Multiple peaks can be evaluated from one chromatogram.
</li>
<li>GPC Summary Result Tables: Displays and prints selected results from all simultaneously displayed chromatograms. Postrun: Automatically displays, prints, exports, and starts other programs after the completion of a measurement.
</li>
<li>Batch: Automatically batch processes, displays, exports, or prints any number of chromatograms.
</li>
<li>Reports: User selectable report sections and WYSIWYG formating of Graphs and Tables.
</li>
</ul>

DataApex CE - Capillary Electrophoresis Extension for Clarity

CE module provides specific terminology, evaluation by time corrected area and peak identification by peak start or end (additionally to peak apex).

<h3>Extension for Capillary Electrophoresis</h3>
The CE Extension activates the CE mode in Clarity environment and can be activated on any <a href="https://lcms.labrulez.com/products/999">Clarity</a> Instrument. CE Extension is compatible also with <a href="https://lcms.labrulez.com/products/1000">Clarity Offline</a> software. CE module provides specific terminology, evaluation by time corrected area and peak identification by peak start or end (additionally to peak apex).
<h4>Main changes in Clarity environment</h4>
<ul>
<li>CE specific terminology</li>
<li>Evaluation by time corrected area</li>
<li>Peak identification by peak start or end (additionally to peak apex).</li>
<li>Additional calculations</li>
</ul>
<h4>CE specific terminology</h4>
The terms used in chromatography mode were substituted by those used in CE:
<ul>
<li>Default mode =&gt; CE mode</li>
<li>Chromatogram =&gt; Electropherogram</li>
<li>Retention time (RT) =&gt; Migration Time (MT)</li>
<li>Column =&gt; Capillary</li>
<li>Mobile Phase =&gt; Electrolyte</li>
<li>Flow Rate =&gt; Power supply</li>
<li>Pressure =&gt; Injection Mode</li>
</ul>
<h4>Separation parameters</h4>
Method Setup allows a user to adjust the Capillary Setting:
<ul>
<li>Total Capillary Length</li>
<li>Length of the capillary.</li>
<li>Effective Capillary Length</li>
<li>Effective capillary length from injection end to the detector position</li>
<li>Separation Voltage</li>
<li>Separation voltage. Allows you to enter also negative values</li>
<li>Reference Peak Mobility</li>
<li>Effective mobility of the EOF reference peak.</li>
</ul>
<h4>Calculations</h4>
The Result Table contains additional columns containing calculations:
<ul>
<li>Apparent Mobility</li>
<li>Effective Mobility</li>
</ul>

DataApex Clarity Chromatography Software

Clarity is a chromatography data software for data acquisition, processing, and instrument control in regulated environment. Clarity is a flexible solution for devices from different vendors, supporting different applications.

Optional control modules provide integrated control of selected instruments such as GCs, LCs, pumps, detectors, autosamplers, etc. Extensions provide functions for specific separation techniques or calculations such as PDA, GPC analysis, Mass spectrometry, or SST. Clarity can run in English, French, German, Russian, Spanish, and Chinese language. Support technicians and developers are close to their users and ready to provide extensive Support from DataApex.
<blockquote>
Ask for <a href="https://www.dataapex.com/product/clarity-demo">Clarity Demo version</a> which allows you to get your hands on software before purchase
</blockquote>
<h3>Main features</h3>
<ul>
<li>Measuring: Simultaneous data acquisition from up to four independent chromatographs, each chromatograph can acquire data from up to 32 detectors.
</li>
<li>Integration: There is an extensive possibility to modify chromatograms. The chromatogram can be changed by entering global parameters or interactively through direct graphic modification of the baseline.
</li>
<li>Overlay: Simultaneously displays a virtually unlimited number of chromatograms and their mathematical modification; for example, mutual deductions or derivations of any order.
</li>
<li>Calibration: Internal and external standard calculation methods, calibration of groups of peaks, and reference peaks method for better identification.
</li>
<li>Wide range of supported instruments: Control modules in Clarity allow users to control various instruments in their lab. See our growing <a href="https://www.dataapex.com/controls">List of supported instruments</a>.
</li>
<li>Extensions completing your workflow: Clarity Extensions integrates your workflow into one application. GPC calculations, PDA data processing, gas or detailed hydrocarbon analyses according to selected norms, and much more.
</li>
<li>Automated measuring support: Sequence tables for any set of samples with or without an autosampler.
</li>
<li>Postrun: Automatically displays, prints, exports, and starts other programs after the completion of a measurement.
</li>
<li>Summary result tables: Displays and prints selected results from all simultaneously displayed chromatograms.
</li>
<li>User settings: User selects parameters for peak display and the specification for axes, including color from an extensive array of color settings. Text labels and lines, either as part of the area or anchored to a chromatogram, may also be inserted.
</li>
<li>Export: Optional exportation of all results, with or without the chromatogram, in various formats, into a file or clipboard.
</li>
<li>Import: Imports chromatograms or mathematical curves, which have been saved in text or AIA formats, from other programs.
</li>
<li>LIMS: Clarity offers connectivity with LIMS, both for sample submission and result output. This can be done via convenient ASCII transfers.
</li>
<li>Method and calibration history: Each chromatogram can easily be displayed under the same conditions as when it was printed, exported, or saved.
</li>
<li>Column performance: Calculations of peaks in terms of symmetry, efficiency, resolution; all by several methods (tangent, moments, etc.).
</li>
<li>Batch: Automatically batch processes, displays, exports, or prints any number of chromatograms.
</li>
<li>User calculations: Users can define custom calculations in the Result and Summary tables. Using the integrated editor, you can create your own columns from original columns and individual mathematical functions.
</li>
<li>User accounts: Sets up access rights and passwords (including their parameters, e.g., minimum length, validity, etc.). Each user can define his or her own appearance of the software.
</li>
<li>Audit trail: Records selected events and operations into a special file. Records selected operations directly into a chromatogram.
</li>
<li>Electronic signature: Each chromatogram can be signed electronically. Signature selection is based on the username or the signature certificate.
</li>
<li>Networked Solution: Clarity chromatography software files can be accessed from networked computers using Clarity Offline software. This enables the offline evaluation of chromatograms, development of new methods, and printing reports. See the <a href="https://gcms.labrulez.com/products/1000">Clarity Offline</a> for more details.
</li>
<li>Language Localizations available: Useful for non-English speakers. At the moment, there are French, German, Russian, Spanish, and Chinese localizations available in a single installation package. Simply switch to your preferred language anytime.
</li>
<li>Competitive approach: The chromatography market offers many specialized HPLC data systems or GC data systems; these are often provided with the purchased instrument. It is usually complicated to integrate such software into the workflow of the laboratory since they do not enable direct control of additional instruments. Compared to other small-scale solutions, Clarity offers a wide range of directly controlled instruments as well as optional Extensions for specific separation techniques. On the other hand, complex solutions with a wide scope of features and scalable design are quite expensive, which is a limiting factor for many customers. Another drawback of the large solutions is their complexity which imposes high demands on users. Compared to this, Clarity represents a scalable medium-ranged solution with a steep learning curve and competitive prices.
</li>
</ul>
<h3>Clarity configurations examples</h3>
<h4>One chromatograph with two detectors</h4>
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Clarity_Chromatograficky_Software_Clarity_configurations_examples_One_chromatograph_with_two_detectors_ae482b83b8/DataApex-Clarity-Chromatograficky-Software-Clarity-configurations-examples-One-chromatograph-with-two-detectors.jpg" alt="DataApex Clarity Chromatography Software: Clarity configurations examples - One chromatograph with two detectors.jpg"/>
<ul>
<li>The HPLC measures on two detectors. Clarity will acquire two separate signals sharing a common timebase (synchronized START/STOP). A resulting chromatogram will contain two signals.</li>
</ul>
<h4>Two chromatographs, one with multiple detectors</h4>
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Clarity_Chromatograficky_Software_Clarity_configurations_examples_Two_chromatographs_one_with_multiple_detectors_b21dc07faf/DataApex-Clarity-Chromatograficky-Software-Clarity-configurations-examples-Two-chromatographs-one-with-multiple-detectors.jpg" alt="DataApex Clarity Chromatography Software: Clarity configurations examples - Two chromatographs, one with multiple detectors.jpg"/>
<ul>
<li>This example displays a configuration with two chromatography systems (GC + HPLC) where the HPLC system uses multiple detectors. All the detectors attached to the HPLC Instrument will share common timebase (synchronized START/STOP). The GC detector will be independent.</li>
</ul>
<h4>Two chromatographs, one digital control</h4>
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Clarity_Chromatograficky_Software_Clarity_configurations_examples_Two_chromatographs_one_digital_control_1bf9cec334/DataApex-Clarity-Chromatograficky-Software-Clarity-configurations-examples-Two-chromatographs-one-digital-control.jpg" alt="DataApex Clarity Chromatography Software: Clarity configurations examples - Two chromatographs, one digital control.jpg"/> This example displays a configuration with two chromatography systems (GC + LC). The GC is connected and controlled via digital interface *, using a GC Control appropriate module.
<h4>Four chromatographs with autosampler each</h4>
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Clarity_Chromatograficky_Software_Clarity_configurations_examples_Four_chromatographs_with_autosampler_each_945873d808/DataApex-Clarity-Chromatograficky-Software-Clarity-configurations-examples-Four-chromatographs-with-autosampler-each.jpg" alt="DataApex Clarity Chromatography Software: Clarity configurations examples - Four chromatographs with autosampler each.jpg"/>
<ul>
<li>This example displays a configuration with two chromatography systems (GC + LC). The GC is connected and controlled via digital interface *, using a GC Control appropriate module.</li>
</ul>
<a href="https://www.dataapex.com/controls">List of supported instruments</a>
<a href="https://www.dataapex.com/product/clarity-std-compatibility">Compatible Windows OS and Hardware</a>
<a href="https://www.dataapex.com/product/clarity-21cfr-compliance">Clarity 21 CFR Part 11 compliance</a>

Products from category Software and libraries from DataApex - page 1

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