<p><strong>He is one of only ten scientists working in Europe who secured the prestigious EMBO Installation Grant this year. After four years in the United States, immunologist Matouš Vobořil recently returned to the Faculty of Science at Charles University to build his own team and advance research focused on the development of immune cells and their training in the thymus. His efforts to combat autoimmune diseases have already caught the attention of numerous grant review panels.</strong></p><h5><strong>Reportedly, one of the motivations for your studies was the awareness that in science, there is still more that is unknown than what is known. You made this statement after receiving the Doctorandus Award for Natural Sciences in 2020, adding that during your lifetime you would like to shift something toward the “known” category. How has that been going so far?</strong></h5><p>The topic for which I&nbsp;take the greatest credit to date is one I&nbsp;began exploring during my doctoral studies and fully developed as a&nbsp;postdoctoral fellow in the U.S., and that is inflammation of the thymus. When you delve into the literature and articles focused on autoimmune diseases, eventually you begin to notice that autoimmune diseases often develop after undergoing some kind of infection. This is particularly evident in connection with long COVID. During inflammatory processes in the body, the immune system responds, and we were interested in whether there is a&nbsp;mechanism that recognises this inflammatory response and teaches T-lymphocytes (immune cells) that this is not a&nbsp;problem, but rather a&nbsp;process inherent to the body.</p><p>During my doctoral studies, I&nbsp;investigated the basic inflammatory response in the thymus, without the presence of actual bacterial or viral inflammation. This turned out to be extremely important. Over time, we discovered that the thymus contains many antiviral molecules and molecules that play a&nbsp;key role in allergic reactions or in the recognition of bacteria and viruses. These molecules create a&nbsp;specific environment in the thymus that mimics what may happen in our bodies later in life, and they train T-cells not to respond to these stimuli. I&nbsp;consider this to be my greatest contribution to the field. Of course, there are still many unexplored areas in this field.</p><h5><strong>The interview I was referring to was published in the magazine of the grammar school where you studied, and which proudly acknowledges your scientific achievements. Was that where your interest in science first began to show?</strong></h5><p>The fact that I&nbsp;studied in Dvůr Králové nad Labem was a&nbsp;huge stroke of luck. Not only is there a&nbsp;zoo, where my parents used to work, so I&nbsp;spent a&nbsp;lot of time there, but thanks to that, I&nbsp;also joined the local Natura club, which brought together people interested in nature and was led by the Dobroruk couple. When I&nbsp;was ten, my parents sent me to a&nbsp;nature-oriented summer camp with them, and I&nbsp;ended up staying with them – which is why I&nbsp;also attended the local high school, where Mrs. Dobroruková taught. She was a&nbsp;wonderful teacher. Her classes really encouraged students to think about what’s&nbsp;happening in nature. Thanks to that, I&nbsp;began participating in biology competitions and got involved in the Czech high school research competition. Although my first scientific experiments focused on ornithology, they gave me the opportunity to present scientific data and meet many people from the Faculty of Science at Charles University, including Professor Jan Černý, who lectured our class on immunology. Suddenly, while still in high school, I&nbsp;realized that this was the path I&nbsp;wanted to take.</p><h5><strong>During your master’s studies, you joined the team of immunologist Dominik Filipp at the Institute of Molecular Genetics of the Czech Academy of Sciences, where you then continued as a doctoral student. How did working with him influence you, and where did it lead you?</strong></h5><p>Dominik Filipp had several ongoing projects related to the peripheral immune response, signalling, and identification of viruses and bacteria. The project I worked on focused on a rare population of cells found in lymph nodes or the spleen. I studied the effect of pathogen-recognising receptors on these cells. Since these cells are similar to those in the thymus and I needed a negative control, I used the thymus for that purpose. To our surprise, the result was not negative but positive. This led us to the phenomenon itself and prompted us to begin investigating its consequences in the thymus.</p><h5><strong>You then travelled overseas to study this discovery – which you actually made rather by chance – in detail. What was your experience like at American research institutions?</strong></h5><p>Amazing. I&nbsp;went to the University of Minnesota to work with particular people, especially my future supervisor, Kristin Hogquist. I&nbsp;had met her at several conferences while I&nbsp;was still in my PhD programme, and I&nbsp;had a&nbsp;feeling that our collaboration could work well both professionally and personally.</p><p>But we were also fortunate to pick Minnesota. It’s&nbsp;a&nbsp;great place to live, and at the same time, excellent science is being conducted there. The Center for Immunology, where I&nbsp;worked, rivals the world’s&nbsp;leading scientific institutions in terms of its research results. I&nbsp;think this is mainly down to the highly supportive environment there, which fosters collaboration. Thanks to this, you can really grow as a&nbsp;scientist there.</p><p>In addition, they focus on explaining and describing the chosen phenomenon as a&nbsp;whole, rather than worrying too much about whether it will result in one or five articles, or whether it will take ten years. Their method of funding supports this approach. In a&nbsp;system of short-term grants, as we know it here, you can’t structure research this way. That’s&nbsp;a&nbsp;major disadvantage for us.</p><h5><strong>How did you develop your own research there?</strong></h5><p>It was there that I&nbsp;fully realized the potential of what we had discovered in the lab in Prague. Kristin Hogquist and her team were working on something similar, but it wasn’t until we teamed up that we were able to take it further. I&nbsp;focused primarily on how various antiviral signals or signals triggered during allergic reactions influence T-cell training and defence against autoimmune diseases following viral infections or allergic reactions. Suddenly, it became clear that this was a&nbsp;vast topic and the foundation for establishing a&nbsp;separate subfield of research on tolerance (the training of immune cells in the thymus so that they do not harm the body while remaining capable of fighting pathogens).</p><p>One great thing was that two labs were coming together at the facility: the one led by Kristin Hogquist and the other led by her husband, Stephen Jameson, which focuses on how different types of infections affect T-cell activation and their response. I&nbsp;realised that these two areas needed to be connected, and I&nbsp;based my own research plan on that – namely, to study how the inflammatory environment, actual inflammation, and viral or bacterial infections can retroactively influence processes in the thymus. This is a&nbsp;topic that no one has addressed yet.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Forum_UK_Voboril_O_imunitnim_systemu_toho_stale_mnoho_nevime_2_b020119f2e.jpg" alt="Forum UK/Petr Jan Juračka: Vobořil: There is still much to learn about the immune system: As head of research, Matouš Vobořil strives to ensure that everyone on his team feels comfortable." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Forum_UK_Voboril_O_imunitnim_systemu_toho_stale_mnoho_nevime_2_b020119f2e.jpg 234w," sizes="100vw" width="1000" height="667"></p><h5><strong>You mentioned how important it was to you that you got along with Kristin Hogquist not only professionally but also on a&nbsp;personal level. To what extent did you take this “personal” aspect into account when putting together your own team at CU SCI?</strong></h5><p>This is tremendously important to me. Kristin Hogquist is not only an outstanding researcher, but also a&nbsp;very kind person. And that really helped me feel at home in the American environment, which sometimes tends to become highly competitive. I&nbsp;realized that I&nbsp;would like those who will one day work on my own team to feel the same way I&nbsp;did on hers.</p><h5><strong>So far, we’ve been talking about what led you to science. Have you, on the other hand, encountered anything during your career so far that has discouraged you from pursuing science?</strong></h5><p>Moving overseas with my family and my two-and-a-half-year-old son during the pandemic wasn’t the easiest thing to do. We had to apply for a&nbsp;national exemption just so that I&nbsp;and my family would be allowed into the U.S. at all. Fortunately, as an immunologist, I&nbsp;fell into a&nbsp;special category subject to less stringent pandemic restrictions. Packing up the family, moving overseas, and learning to navigate a&nbsp;completely different system is undoubtedly a&nbsp;major challenge. It required sacrifices not only from me, but above all from my wife, who had to put her own career on hold for several years because of mine. This is one of the biggest and most demanding obstacles that scientists and their families must overcome.</p><p>The second major obstacle you have to deal with as a&nbsp;scientist is paperwork – something I’ve only fully realized now that I’m leading a&nbsp;research group. Even though you hear about it from those around you, it still doesn’t prepare you for when it comes. As a&nbsp;trainee, you do science and conduct experiments in the lab, but suddenly everything shifts, and you become a&nbsp;manager and administrator of all sorts of things. I&nbsp;spend about 30 percent of my time on paperwork. It’s&nbsp;not exactly fun.</p><h5><strong>You obtained a&nbsp;Primus grant, a&nbsp;Junior Star grant from the Czech Science Foundation, and most recently an EMBO Installation Grant. What research challenges do you now face with these grants?</strong></h5><p>I&nbsp;would also like to apply for an ERC Starting Grant this year as well. In the Junior Star project, we are studying cell migration to the thymus. We hypothesize that so-called dendritic cells migrate to the thymus from the periphery (skin, lungs, intestines) – that is, from sites exposed to the external environment and inflammation. These cells are thought to bring information about their own antigens to the thymus and teach developing T-cells tolerance. We aim to determine whether this migration actually occurs, under what circumstances, and how important it is for establishing tolerance to specific tissues. This could help answer the question of why autoimmune skin diseases, such as psoriasis, develop following inflammatory processes.</p><p>The second objective is broader. We would like to answer a&nbsp;major question in immunology: <strong>why do autoimmune diseases develop after a&nbsp;person has had an infection? </strong>We want to study how different types of inflammation (viral, bacterial, or yeast infections) affect the training of immune cells in the thymus.</p><p>We would like to introduce a&nbsp;system of so-called “dirty mice.” The entire field of immunological research is based on working with mice raised in sterile conditions so that we can easily manipulate them and observe how these manipulations affect the immune system. In reality, however, the immune system does not function this way. I&nbsp;brought this idea back from the University of Minnesota, where they placed standardized mice in the same cage with mice purchased from various pet stores around Minneapolis. After a&nbsp;few weeks to months, the mice contract almost everything the store-bought mice have, thereby developing a&nbsp;true physiological immune response. Yet they are still the same mice – genetically identical – that we can manipulate. This is an excellent system that allows us to study immune responses in a&nbsp;much more physiological context.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Forum_UK_Voboril_O_imunitnim_systemu_toho_stale_mnoho_nevime_3_c458457e12.jpg" alt="Forum UK/Petr Jan Juračka: Vobořil: There is still much to learn about the immune system " srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Forum_UK_Voboril_O_imunitnim_systemu_toho_stale_mnoho_nevime_3_c458457e12.jpg 234w," sizes="100vw" width="1000" height="667"></p><h5><strong>Will you be applying for a&nbsp;European Research Council (ERC) grant with that goal in mind?</strong></h5><p>Exactly.</p><h5><strong>In order to succeed in the competition for ERC grants, the projects should push the boundaries of knowledge, which also involves a&nbsp;certain degree of risk. Where do you see the greatest risks in your own research?</strong></h5><p>There are many risks. One of the biggest is that although all the infections we plan to introduce are controlled and well-documented, you still never have full control over them. So it’s&nbsp;possible that not only will the mice become peripherally infected, but the thymus itself will also become infected, which could complicate the experiments. At the same time, this is a&nbsp;physiological system – and I’m talking mainly about the “dirty mice” – which means that each mouse will respond a&nbsp;little differently, and that will generate enormous variability in the samples. Immunologists strive to have the purest system possible, so that when they introduce, for example, a&nbsp;single infectious agent, they can then observe exactly what’s&nbsp;happening there. In this regard, we are actually taking a&nbsp;step back, so to speak, because we want it to be more variable and closer to reality. Setting up and analysing data from such experiments so that they’re reproducible and reveal a&nbsp;real phenomenon can be a&nbsp;real challenge. But that’s&nbsp;the only way we can get closer to real life.</p><h5><strong>The most recent Nobel Prize in Physiology or Medicine was awarded to three immunologists: Mary E. Brunkow, Fred Ramsdell, and Shimon Sakaguchi, who recently gave a&nbsp;lecture in Prague. Did you meet him? How much did awarding the Nobel Prize to immunologists motivate you further in your work?</strong></h5><p>When Shimon Sakaguchi was in Prague, I&nbsp;was still in the U.S., but I&nbsp;did meet him several times at various conferences and even had the opportunity to talk with him on multiple occasions, given that we’re both involved in T-cell research. In our community, people have long been placing bets on when they’ll finally get the Nobel Prize. For me, their discoveries are truly inspiring, but the Nobel Prize itself doesn’t motivate me that much anymore. I&nbsp;find the story behind it to be more interesting. It took a&nbsp;very long time for the scientific community to accept their findings. One of the seminal articles was published in the <i>Journal of Immunology</i>, which isn’t a&nbsp;journal with as high a&nbsp;profile as <i>Nature</i> or <i>Science,</i> and not one where you’d expect to read about such a&nbsp;groundbreaking discovery. It took several years before it became clear just how significant this discovery was. Now I&nbsp;often remind my students of this – even an article in the <i>Journal of Immunology</i> can win you a&nbsp;Nobel Prize, and that is incredibly inspiring.</p><blockquote><h5><strong>Matouš Vobořil, PhD</strong></h5><p>Graduate of the Faculty of Science at Charles University. His research focuses on the development of immune cells in the thymus, the onset of autoimmune diseases, and the function of antigen-presenting cells. After spending four years as a&nbsp;postdoctoral fellow at the University of Minnesota on Kristin Hogquist’s&nbsp;team, he returned to Europe in 2025. Thanks to a&nbsp;Primus grant from Charles University, he established his own research group at the Faculty of Science. He subsequently received a&nbsp;Junior Star grant from the Czech Science Foundation and, this January, an EMBO Installation Grant. For his dissertation, he was awarded the Doctorandus Prize as part of the Česká hlava initiative.</p></blockquote>

Vobořil: There is still much to learn about the immune system 

<h3><strong>How are PFAS regulations changing, and what role will ion chromatography play in the future of environmental testing?</strong></h3><p>In this episode, &nbsp;David interviews <strong>Jay Gandhi, PhD, </strong>Vertical Markets Manager at <strong>Metrohm USA</strong>, for an in-depth discussion on PFAS analysis, the rise of AOF (Adsorbable Organic Fluorine) testing, and the development of EPA 1621 and ISO 18127 standards.</p><p>With more than 30 years of experience in ion chromatography, Jay shares valuable perspective on how the field has evolved—from early applications and NASA water recovery projects to today’s challenges involving PFAS, TFA, and emerging contaminants.</p><h4><strong>Topics covered in this episode include:</strong></h4><ul><li>What PFAS are and why they matter</li><li>The difference between targeted PFAS methods and AOF analysis</li><li>How combustion ion chromatography works</li><li>Behind the scenes of EPA 1621 and ISO 18127 method development</li><li>Regulatory trends in water, textiles, and food packaging</li><li>TFA analysis using IC-MS and IC-MS/MS</li><li>The future of ion chromatography in environmental labs</li></ul><h3><strong>Video Transcription</strong></h3><p>For more than three decades, Jay Gandhi has worked with ion chromatography (IC), watching the technique expand from a specialized tool for water analysis into an analytical platform used across environmental testing, food and beverage analysis, semiconductor manufacturing, battery applications, and, increasingly, PFAS analysis.</p><p>In an interview for <i>Concentrating on Chromatography</i>, Gandhi discusses his introduction to IC during his work on a NASA Mars exploration project, the emergence of PFAS as a major analytical challenge, and why techniques such as adsorbable organic fluorine (AOF) determination and combustion ion chromatography (CIC) can provide information that targeted LC-MS analysis alone cannot deliver. He also examines the development of standardized methods, sample preparation challenges, and the future role of IC-MS and total fluorine approaches in PFAS monitoring.</p><h4><strong>From NASA to ion chromatography</strong></h4><p>Gandhi's introduction to ion chromatography came through his work as a principal scientist on a NASA Mars exploration project focused on water recovery under zero-gravity conditions. IC played an important role because it enabled researchers to establish the ionic balance of anions and cations in water.</p><p>The technology was used both to investigate micronutrients relevant to agricultural applications and to evaluate water purity for potential astronaut consumption. During approximately three years of this work, Gandhi gained extensive experience with ion chromatography. This ultimately led him deeper into IC instrumentation and, 24 years ago, to joining Metrohm.</p><p>At the beginning of his career, IC was strongly associated with relatively straightforward anion and cation analysis in water. The technique itself had been used for water analysis since the 1970s, but Gandhi has seen its application range expand dramatically.</p><p>Food and beverage testing and environmental analysis became important fields, supported by both direct and indirect detection strategies. More recently, IC has also found applications in areas such as the semiconductor industry and battery recycling.</p><p>In Gandhi's words, ion chromatography has effectively "bloomed" into numerous application areas.</p><h4><strong>PFAS changes the analytical challenge</strong></h4><p>PFAS represent a particularly important chapter in this development. These chemicals have been used for decades in numerous consumer and industrial products, including non-stick materials, firefighting foams, water-resistant textiles and other applications.</p><p>Gandhi recalls work on PFOA and PFOS using ion chromatography with conductivity detection as early as 2008. However, the achievable detection limits were insufficient for the extremely low concentrations that later became important in PFAS analysis.</p><p>A major turning point for him came in 2015, when he encountered research from Sweden using <strong>combustion ion chromatography to investigate total fluorine</strong>. Subsequent collaboration with researchers at Clarkson University and Harvard University, particularly on aqueous film-forming foam (AFFF), further demonstrated the importance of looking beyond individual targeted PFAS compounds.</p><h4><strong>Why targeted LC-MS does not tell the whole story</strong></h4><p>Targeted LC-MS is highly sensitive and selective and can provide detailed information about individual PFAS compounds. However, according to Gandhi, the number of possible PFAS structures in the environment is vastly greater than the number routinely included in targeted methods.</p><p>A targeted method may monitor dozens or perhaps around one hundred compounds, while the overall PFAS universe can include thousands of chemical structures. Consequently, targeted analysis may characterize only a small fraction of the total PFAS burden.</p><p>There are other practical considerations. LC-MS measurements can be affected by matrix-dependent ion suppression, while accurate quantification frequently relies on isotope-labelled internal standards. Such standards are available for only a limited number of compounds and can be expensive.</p><p>This is where measurements of total or adsorbable organic fluorine can provide complementary information. Rather than asking <i>which specific PFAS compounds are present?</i>, these approaches can help answer a broader question: <i>how much fluorine associated with this chemical space is present in the sample?</i></p><h4><strong>AOF as a complementary approach</strong></h4><p>Adsorbable organic fluorine analysis provides a different perspective from targeted LC-MS. In the workflow discussed by Gandhi, organic fluorine compounds are captured during sample preparation and subsequently measured using combustion ion chromatography.</p><p>The principle of CIC builds upon older total organic halogen analysis. The sample is combusted at temperatures above approximately 1,000 °C, breaking carbon-halogen bonds. In PFAS-related analysis, carbon-fluorine bonds are broken and the resulting fluoride is collected in an absorption solution.</p><p>Ion chromatography is then used to separate and quantify the fluoride.</p><p>Replacing older detection approaches with IC provides both sensitivity and selectivity for the halogens being measured. Effective combustion is critical: oxygen supports the combustion process, while a carrier gas transports the products into the absorption solution for subsequent IC analysis.</p><h4><strong>The challenge of inorganic fluoride</strong></h4><p>The broad response of CIC is simultaneously one of its strengths and one of its analytical challenges. Combustion does not distinguish fluorine originating from PFAS from fluorine present in inorganic compounds such as fluoride salts.</p><p>This becomes particularly important when analyzing water containing relatively high concentrations of inorganic fluoride while attempting to quantify organic fluorine at very low levels.</p><p>Sample preparation therefore has a critical role. Inorganic fluoride must be effectively separated from the fraction of interest, while materials used during sample preparation must themselves have sufficiently low fluoride backgrounds.</p><p>Contamination can come from unexpected sources. Gandhi points out that background fluoride may originate not only from reagents and sample preparation materials but potentially from the laboratory environment. Careful blank control, appropriate materials and rigorous evaluation of interferences are therefore essential when moving toward increasingly low detection limits.</p><h4><strong>From research method to international standardization</strong></h4><p>The development of standardized AOF methods illustrates the importance of collaboration between academia, industry, regulatory organizations and analytical laboratories.</p><p>Gandhi describes work that began in Europe around 2015 and subsequently progressed through German standardization activities, ISO development, ASTM-related collaboration and the U.S. EPA. The process eventually contributed to methods such as <strong>EPA Method 1621</strong>.</p><p>He emphasizes that this was not the work of a single scientist or organization. Developing a robust method required years of experiments, discussions and sometimes difficult technical debates among numerous stakeholders.</p><p>For Gandhi, the essential principle was that experimental evidence ultimately had to determine the outcome. Collaboration becomes possible when scientists focus on the data rather than the organizations they represent.</p><h4><strong>PFAS monitoring is moving beyond drinking water</strong></h4><p>Regulatory attention to PFAS is also expanding beyond drinking water. Gandhi describes a broader strategy that begins with reducing the manufacture and use of PFAS-containing materials and continues with removing existing contamination from the environment.</p><p>Wastewater represents an important part of this picture because PFAS can enter it from numerous sources. Historical contamination from landfills and contaminated sites can also migrate into groundwater and ultimately affect drinking-water supplies.</p><p>Consumer products are another area of increasing attention. Food packaging, disposable containers, automotive fabrics, outdoor clothing and water-repellent textiles have historically used fluorinated substances to provide properties such as grease, water or stain resistance.</p><p>Reducing PFAS use in such products could therefore gradually decrease the amount entering waste streams and the wider environment.</p><h4><strong>Screening first, regulation later?</strong></h4><p>Gandhi expects AOF to be particularly valuable as a <strong>screening tool</strong>, providing an estimate of broader fluorine contamination before laboratories proceed to more specific analyses.</p><p>Its importance becomes clear when AOF results are compared with targeted PFAS measurements. Gandhi reports that laboratories working with EPA Method 1621 have observed differences between targeted PFAS results and broader AOF measurements ranging from approximately <strong>300- to 4,000-fold in the total fluorine mass balance</strong>.</p><p>Such discrepancies suggest that targeted methods can leave a substantial portion of fluorine unexplained.</p><p>Rather than competing with LC-MS, AOF and CIC therefore provide complementary information. A broad screening method can reveal the magnitude of total contamination, while targeted mass spectrometry identifies and quantifies specific compounds of interest.</p><h4><strong>Where IC-MS fits into the PFAS toolbox</strong></h4><p>No single technique can cover the entire PFAS problem. Gandhi highlights very short-chain, highly polar fluorinated compounds as another analytical challenge.</p><p>Compounds such as trifluoroacetic acid (TFA) are highly water-soluble and may not be quantitatively retained by the carbon materials used for AOF sample preparation. Direct ion chromatography can provide an alternative route for separating such compounds from common inorganic anions.</p><p>Coupling IC with mass spectrometry adds another level of sensitivity and selectivity. Gandhi therefore sees <strong>IC-MS and IC-MS/MS</strong> as increasingly important tools for highly polar fluorinated compounds. Similar approaches can also be useful beyond PFAS, including the determination of polar pesticides such as glyphosate and glufosinate.</p><h4><strong>Toward lower detection limits and more complete PFAS analysis</strong></h4><p>For Gandhi, current standardized methods represent a beginning rather than an endpoint. Improvements in instrumentation and particularly sample preparation could push total fluorine analysis to substantially lower concentrations.</p><p>He notes that current combustion IC configurations can reach approximately <strong>0.5 ppb</strong>, or 500 parts per trillion, and believes that improvements in sample volume, preparation procedures and mitigation of inorganic fluoride backgrounds could eventually move detection below 100 ppt and potentially toward 50 ppt.</p><p>Extractable organic fluorine workflows could provide another bridge between broad fluorine screening and targeted LC-MS methods. Combining improved extraction with CIC could allow samples to be screened for organic fluorine before more detailed compound-specific characterization.</p><p>The broader message from Gandhi's career is that PFAS analysis is unlikely to be solved by a single analytical technique. <strong>Targeted LC-MS provides compound-specific sensitivity and selectivity; AOF and combustion IC reveal a broader fluorine picture; and IC-MS can address highly polar compounds that are difficult to capture using conventional workflows.</strong> Used together, these techniques can provide laboratories with a much more complete understanding of PFAS contamination than any one approach alone.</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>

The Future of Ion Chromatography | PFAS Testing, EPA 1621 & AOF Explained

<p><strong>In late February 2025, a train carrying benzene derailed in Hustopeče nad Bečvou, and within hours, a race was on to save the groundwater and surface water. One of the most toxic industrial substances began seeping into the gravel-sand subsoil. While fieldwork was underway to prevent the spread of contamination, decisions were already being made in the CXI TUL laboratories regarding how to subsequently clean up the contaminated rock environment.</strong></p><p>The accident ranks among the <strong>most serious environmental incidents in the Czech Republic in recent years</strong>. After a tanker train derailed, hundreds of<strong> metric tons of benzene leaked</strong>; due to the highly permeable geological subsoil, it quickly seeped into deeper soil layers and into the groundwater. The combination of the substance’s high toxicity and local conditions complicated both the emergency response and the subsequent remediation. The key was to stop further spread, determine the extent of the contamination, and establish a remediation strategy for the entire site.</p><p>It was at this stage that CXI TUL became involved in the solution. At the request of the renowned remediation company DEKONTA, a.s., a team led by <strong>RNDr. Jan Němeček, Ph.D.</strong>, began testing the feasibility of the<strong> in situ chemical oxidation (ISCO) method</strong>. This technology is designed to<strong> break down benzene directly within the rock matrix</strong>, without the need for extensive excavation of contaminated soil or the pumping out of large volumes of groundwater. The goal was simple: to find a method that would work quickly, safely, and under the actual conditions of the affected site.</p><h4><strong>Benzene Remediation: Technically Simple, Complicated in Practice</strong></h4><p>Benzene is a highly toxic and carcinogenic substance that rapidly penetrates into groundwater in permeable subsoil, where it dissolves and spreads further as the water flows toward surface water bodies. Benzene also binds to rock particles and migrates in the form of vapors into overlying unconsolidated layers.</p><p>Scientists in Liberec therefore tested <i>in situ </i>chemical oxidation (ISCO) technology under laboratory conditions. The goal was to find an oxidant capable of breaking down benzene directly underground into less hazardous substances.</p><p>The tests evaluated two main options:<strong> activated hydrogen peroxide and sodium peroxodisulfate</strong>. Both substances removed up to<strong> 99.99% of the benzene</strong>, but there was a difference in their kinetics and impacts on the natural environment. Activated hydrogen peroxide achieved nearly complete degradation of the contaminant within a single day. Activated sodium peroxodisulfate was slower and also significantly altered the chemistry of the water; it acidified the environment and increased the sulfate content in the water, which poses an additional environmental burden.</p><p>For field applications, the researchers therefore unequivocally recommended <strong>activated hydrogen peroxide</strong>.</p><h4><strong>Dosage Matters</strong></h4><p>It was not just the oxidant’s effectiveness that was key. It was equally important to determine how the chemical reaction would behave in a real geological environment. The team of scientists therefore also analyzed what is known as <strong>soil oxidant consumption (SOD)</strong>. It turned out that a significant portion of the oxidizing agent does not react solely with benzene but is also consumed to a significant extent by the rock environment itself, particularly by natural organic substances present in the fine-grained fraction of the soil.</p><p>An oxidant consumption value was determined specifically for the local composition of the aquifers, which is essential for the correct dosing of chemicals in the field so that the remediation is not only effective but also economically viable and safe for surrounding ecosystems.</p><h4><strong>One Year After the Accident: Research Turns into Real-World Assistance</strong></h4><p>While the public often perceives university science as a distant world of laboratories and grant projects, it is precisely situations like this that demonstrate its practical impact. The results of the work by researchers at CXI TUL did not remain confined to academic studies but directly influenced decisions regarding the technology used to clean up one of the largest environmental accidents in recent years.</p>

Science on the Front Lines: Cleanup of a Benzene Spill

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Thermo Scientific mzCloud Mass Spectral Library

mzCloud is a high-resolution, accurate-mass MSⁿ spectral library that helps identify unknown compounds when no reference standards are available, especially in complex studies.

<div colctrl-id="1-1"><div><div container-id="cq-colctrl-lt8" comp-id="B1"><div><h3><strong>Confident identification for unknown small molecules</strong></h3></div></div><div container-id="cq-colctrl-lt8" comp-id="B2"><div><p><strong>Mass spectral libraries and databases may be required to identify unknown compounds when reference standards are not available. This is particularly true for studies in areas such as metabolomics, forensic toxicology, food &amp; beverage, environmental emerging contaminants or extractables &amp; leachables.</strong></p></div></div></div></div><div><p>In these situations, a mass spectral library, particularly a high-resolution and accurate-mass MS<sup>n</sup> fragmentation library, such as the mzCloud mass spectral library, can provide the information required to confidently identify unknown compounds.</p><h3><strong>Key benefits</strong></h3><h5><strong>Confidence for unknown identification</strong></h5><p>Comprehensive curation of all library content with extensive, fully annotated and searchable fragmentation spectra to provide confidence in your results.</p><h5><strong>Know more unknowns&nbsp;&nbsp;&nbsp;&nbsp;</strong></h5><p>Identify unknowns with automated deconvolution and library searching against extensive fragmentation spectra covering a wide chemical space, including small molecule applications.</p><h5><strong>From spectra to structure&nbsp;&nbsp;</strong></h5><p>With solutions to cover infusion or LC-MS, nominal or high-resolution data, you can be sure that your MS<sup>n</sup> spectra will provide you with actionable results, even when there is no spectral library match.</p><h5><strong>Flexibility for research and routine applications</strong></h5><p>Search for free online at <a target="_blank" rel="noopener noreferrer" href="http://www.mzcloud.org/" aria-label="mzCloud.org - open in a new tab" data-uw-rm-ext-link="" uw-rm-external-link-id="http://www.mzcloud.org/$mzcloud.org"><span style="white-space:nowrap;">mzCloud.org</span></a>, or directly access through the Thermo Scientific Compound Discoverer and Mass Frontier software packages. Not online? mzVault provides you with the ability to perform offline spectral library searching.</p><figure class="image"><img style="aspect-ratio:1398/1002;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_ecc79fe9bf.jpg" alt="Thermo Scientific mzCloud Mass Spectral Library: mzCloud is easily and freely accessed online. Anyone can search, review, and use its extensive information. Note that the numbers above were correct at time of publication. For the most up to date numbers visit mzCloud.org." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_ecc79fe9bf.jpg 218w," sizes="100vw" width="1398" height="1002"></figure><h3><strong>What is in the mzCloud mass spectral library?</strong></h3><div style="height:auto;" id="whatismzcloud"><div><div><div><div><p>mzCloud is an extensively curated, high-quality mass spectral fragmentation library that contains significant amounts of spectra and metadata for each entry. Each entry also includes exhaustive high-resolution <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/cz/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/mass-spectral-libraries/mzcloud-mass-spectral-library.html?open=multi-stage-fragmentation#multi-stage-fragmentation">MS/MS and multi-stage MS<sup>n</sup> spectra</a>, which have been acquired at various collision energies and using different fragmentation techniques.</p><p><strong>Each raw mass spectrum</strong> has been filtered to remove noise, recalibrated to ensure absolute mass accuracy, fully annotated and <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/cz/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/mass-spectral-libraries/mzcloud-mass-spectral-library.html?open=content-curation#content-curation">curated</a> to ensure quality and consistency.</p><p>Finally, the contents of the library are <strong>updated weekly</strong> to provide coverage of a wide chemical space, ensuring relevance to all small-molecule application areas.</p></div><div><figure class="image"><img style="aspect-ratio:740/410;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_2_77a6795676.jpg" alt="Thermo Scientific mzCloud Mass Spectral Library: Example of the Mass Frontier software utilizing the contents of mzCloud to identify an unknown compound through a sub-structural search; the experimental fragmentation spectrum (top left) is searched against the mzCloud mass spectral database, with corresponding spectral hits shown in a given spectral tree (top, middle), with supporting spectral information (bottom left) and the identified precursor structure from the matched fragmentation spectra (bottom right), and the library compound structure from which the fragment originated (top right)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_2_77a6795676.jpg 245w," sizes="100vw" width="740" height="410"></figure></div><div><p>Distinguishing among types of databases is important, as the contents and quality of the contents typically differs significantly and may have an impact upon the reliability of the data and the confidence in any results obtained.</p><ul><li><strong>Chemical database</strong>: A collection of chemical information with, at minimum, a name and a formula. It may also include structures, elemental composition, retention time information, and additional biological or chemical metadata.</li><li><strong>Accurate-mass (AM) database</strong>: An AM database contains accurate mass formulas.</li><li><strong>Accurate-mass retention-time (AMRT) database</strong>: An AMRT database contains accurate mass and retention time(s) for specific analytical methods.</li><li><strong>Library</strong>: A library is a database (AM or AMRT) that, in addition to the above, also contains reference mass spectral data, MS/MS, and/or MS<sup>n</sup> data on compounds.</li></ul><h3><strong>Multi-stage fragmentation in the mzCloud mass spectral library</strong></h3><div style="height:auto;" id="multistagefragmentation"><div><div><div><div><figure class="image"><img style="aspect-ratio:740/420;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_3_792a9d9a59.jpg" alt="Thermo Scientific mzCloud Mass Spectral Library: A schematic representation of a spectral tree within mzCloud. The MS spectra are acquired for a given compound in multiple polarities (ESI +/-), and for a range of adducts. Each precursor is exhaustively fragmented using different fragmentation techniques (CID, HCD) and at multiple collision energies to produce collections of fragmentation spectra at each fragmentation level (MS2, MS3, MS4 etc.), generating a comprehensive spectral tree of information for each library entry." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_3_792a9d9a59.jpg 245w," sizes="100vw" width="740" height="420"></figure><p>mzCloud is an<strong> all-encompassing mass spectral library </strong>with content based on a wide chemical space (therefore covering all small-molecule application areas), and acquiring high-resolution and accurate-mass data at various collision energies, for multiple adducts, using CID and HCD. Approximately 10–20 collision energies are included for every precursor ion; this multi-stage, multidimensional MS<sup>n</sup> spectral data are arranged into spectral trees, which are both extensive and comprehensive, typically containing many hundreds to thousands of spectra for each compound, with many exceeding MS<sup>4</sup> fragmentation steps.</p><p>The extensive data for each library entry is critical for accurate compound identifications, matching experimentally obtained data to that of the library contents, with fit confidence and data visualization <strong>provided in the</strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong> Compound Discoverer</strong></a><strong> and </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong>Mass Frontier</strong></a><strong> data analysis software.</strong> Additional tools in Compound Discoverer and Mass Frontier software, including <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1762"><strong>mzLogic</strong></a>, use the extensive fragmentation information to confidently identify unknowns that cannot be identified based upon the spectral library compound entries alone.</p><h3><strong>Content curation in the mzCloud mass spectral library</strong></h3><div style="height:auto;" id="contentcuration"><div><div><div><div><figure class="image"><img style="aspect-ratio:740/342;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_4_c7064c2ca2.jpg" alt="Thermo Scientific mzCloud Mass Spectral Library: An example of the mass spectral content curation tool available within the Mass Frontier software. It contains all the functionality used to manually curate the content contained within mzCloud. The power of mzCloud lies in both the extent and high quality of its content, which helps make confident compound identifications." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_4_c7064c2ca2.jpg 245w," sizes="100vw" width="740" height="342"></figure><p>Despite the fact that <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;manufacturerItems=3&amp;search=orbitrap"><strong>Thermo Scientific Orbitrap-based mass analyzers</strong></a> routinely deliver sub 3-ppm mass errors, there is a small amount of inaccuracy in any experimental data used to search against a library; these errors would be compounded if the library itself also contained data with mass errors. The compounded errors would mean that any identifications could be harder to make or have lower confidence due to match scores being higher.</p><p>Curating the content within mzCloud guards against error and variability in the reference spectra against which data is compared. <strong>The process of curation involves:</strong></p><ul><li>Averaging multiple, individually acquired spectra</li><li>The removal of mass spectral noise</li><li>Recalibration of the mass spectra based upon the predicted formulas for the fragment ion elemental compositions, based upon the known elemental composition and structure of the precursor ion</li><li>Annotation of all fragment ions with the fragment structure</li><li>Addition of large amounts of metadata, including the source of the data and all original raw data files</li></ul><p>This curation process is performed <strong>for every spectra</strong> - every collision energy, every fragmentation type, every MS<sup>n</sup> level and for each precursor ion. As such, the spectral data in mzCloud is of <strong>exceedingly high quality </strong>and offers significant advantages over crowd-sourced libraries due to the high levels of control.</p><figure class="image"><img style="aspect-ratio:740/350;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_5_0c3fdc4c6c.jpg" alt="Thermo Scientific mzCloud Mass Spectral Library: A recalibrated fragmentation spectrum showing no error on the highlighted peak at m/z 213.05462, along with all of the annotation that is provided for each spectra, at each collision energy, for each fragmentation type at each MSn level." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_5_0c3fdc4c6c.jpg 245w," sizes="100vw" width="740" height="350"></figure><div><div><div container-id="cq-colctrl-lt8" comp-id="B1"><div><h3><strong>How can I use the mzCloud mass spectral library?</strong></h3><p>Accelerate your small molecule unknown identification studies with <strong>mzCloud</strong>, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1762"><strong>mzLogic</strong></a>, and the other data analysis and mass spectral prediction tools available in<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer</strong></a> software and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong>Mass Frontier</strong></a><strong> </strong>software.</p><p><img style="aspect-ratio:860/261;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_7_a8cefb0028.jpg" alt="Thermo Scientific mzCloud Mass Spectral Library: Connectivity of mzCloud and mzVault to Mass Frontier." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_7_a8cefb0028.jpg 245w," sizes="100vw" width="860" height="261"></p><p>The content within mzCloud is accessible through Compound Discoverer and Mass Frontier software packages, provided you have an internet connection. No internet? No problem – <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1760"><strong>mzVault</strong></a>, provides you with the MS and MS/MS content of mzCloud in an offline format.</p><div style="height:auto;" id="accessmzcloud"><div><div><div><div colctrl-id="3-1"><div><div container-id="cq-colctrl-lt8" comp-id="B1"><div><p><img style="aspect-ratio:860/242;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_6_ae3c0a28e1.jpg" alt="Thermo Scientific mzCloud Mass Spectral Library: Connectivity of mzCloud and mzVault to Compound Discoverer." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_6_ae3c0a28e1.jpg 245w," sizes="100vw" width="860" height="242"></p><p>Due to security concerns or local firewalls, not everyone can connect processing PCs to the internet. With that in mind, the contents of mzCloud are combined into an offline version twice a year. The <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1760"><strong>mzVault</strong></a><strong> </strong>software application helps you access this information. In addition to accessing the offline version of mzCloud, the mzVault application can store and search your high-quality custom in-house (offline) MS/MS spectral libraries.</p></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>

Products from category LCMS libraries distributed by Thermo Fisher Scientific (EMEA) - page 1

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