<div><div><div><p><strong>Scientists at IOCB Prague have developed a breakthrough technology that streamlines aptamer development. The new method integrates several biochemical and bioinformatics steps and paves the way for new diagnostic and therapeutic applications. Ongoing applications include wearable sensors that monitor selected biomarkers in real time and provide early warnings of impending health complications. The findings were published in </strong><i><strong>Nature Communications</strong></i><strong>.</strong></p></div></div><div><p>Aptamers are short DNA or RNA strands that can recognize and bind to a specific target molecule with high precision. Similar to antibodies, they can be used to detect these molecules or modulate their activity. Unlike antibodies, they are much more stable, can be produced synthetically, and can be chemically modified to achieve the desired properties. As a result, they can offer capabilities that cannot be achieved with antibodies.</p></div><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Nova_technologie_inovuje_vyvoj_aptameru_syntetickych_alternativ_protilatek_2_81e99b9900.jpg" alt="IOCHB Prague: New technology streamlines the development of aptamers, synthetic alternatives to antibodies: Chemically modified DNA aptamer bound to the target protein." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Nova_technologie_inovuje_vyvoj_aptameru_syntetickych_alternativ_protilatek_2_81e99b9900.jpg 228w," sizes="100vw" width="1343" height="916"></p><p>As demand grows for accurate and rapid diagnostic tools, aptamers are often better suited to these applications than antibodies. However, developing aptamers is both experimentally demanding and time-consuming. A team of scientists from IOCB Prague, led by Dr. Marek Ondruš and <a target="_blank" rel="noopener noreferrer" href="https://hocek.group.uochb.cz/en"><strong>Prof. Michal Hocek</strong></a>, has now developed a technology that significantly shortens the development process.</p><p><i>“Developing an aptamer is often like looking for a needle in a haystack. Among trillions of different DNA sequences, we search for the one that binds strongly and specifically to a target molecule. Our new approach first screen for ‘aptamer families’ – hundreds of related sequences – and then identify the best-performing member of the family. This approach can reduce development time from several months to only a few days,” </i>says Marek Ondruš.</p><blockquote><p><strong>Video:</strong><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=_3zXUeVMugU"> New technology streamlines the development of aptamers, synthetic alternatives to antibodies&nbsp;</a></p></blockquote><p>The team has also expanded the potential applications of aptamers by chemically modifying their building blocks. For example, introducing functional groups similar to those found naturally in amino acids allows the resulting molecules to combine the advantages of both DNA and antibodies: Their sequence is encoded by the order of nucleotides in DNA, while the attached chemical modifications greatly expand their ability to recognize biologically relevant targets and mimic interactions between proteins that are underlying many biological processes.</p><p>The researchers demonstrated the potential of this new method using the human insulin receptor, a key protein that regulates blood sugar levels. They developed an aptamer that specifically binds to the receptor and elucidated the molecular basis of this interaction using cryo-electron microscopy. <i>“We have shown that chemically introduced functional groups play a crucial role not only in target recognition and formation of the aptamer–protein complex, but also in stabilizing the DNA aptamer’s structure. Our findings provide new insights into how chemically modified nucleic acids can mimic key properties of proteins,”</i> says Marek Ondruš.</p><p>In the future, the technology could complement – or, in some applications, even replace – antibody-based diagnostic tools. Researchers are collaborating with <a target="_blank" rel="noopener noreferrer" href="http://iocbtech.cz/">IOCB Tech</a> on its further development, as the company helps to bring discoveries from IOCB Prague into practical applications.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Nova_technologie_inovuje_vyvoj_aptameru_syntetickych_alternativ_protilatek_9694c21671.jpg" alt="IOCHB Prague/Tomáš Belloň: New technology streamlines the development of aptamers, synthetic alternatives to antibodies: Dr. Marek Ondruš, first author of the study, and Prof. Michal Hocek, head of the Bioorganic and Medicinal Chemistry of Nucleic Acids research group at IOCB Prague." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Nova_technologie_inovuje_vyvoj_aptameru_syntetickych_alternativ_protilatek_9694c21671.jpg 234w," sizes="100vw" width="2000" height="1335"></p><blockquote><h4><strong>Original article</strong></h4><h4><a target="_blank" rel="noopener noreferrer" href="https://www.nature.com/articles/s41467-026-73676-y#citeas"><strong>Expedient single-round selection of hyper-modified aptamer targeting insulin receptor from over-represented dually nucleobase-modified DNA libraries</strong></a></h4><p>ablo Alberto Franco-Urquijo, Marek Ondruš, Jaroslav Kurfürst, Jana Škerlová, Irena Selicharová, Lucie Mužíková Čechová, Hana Šváchová, Alena Semerádtová, Anatolij Filimoněnko, Adéla Fejfarová, Jiří Homola, Tomáš Kouba &amp; Michal Hocek</p><p><i><strong>Nat. Commun., 2026</strong></i></p><p><a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1038/s41467-026-73676-y"><span>https://doi.org/10.1038/s41467-026-73676-y</span></a><span>&nbsp;</span></p><h6>licenced under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6></blockquote><h4><strong>Abstract</strong></h4><p>Discovery of functional nucleic acids from randomized libraries typically relies on multiple, time-consuming iterative rounds of in vitro selection with low success rate. Here, we present a single-round selection strategy for rapid screening of multiple over-represented nucleobase-modified DNA libraries and various selection conditions, capable of identifying high-affinity modified aptamers. Double partition followed by amplification of eluted sequences, NGS analysis and clustering provides fast identification of aptamer candidates. Screening of modified DNA libraries containing modified adenine and uracil nucleotides bearing hydrophobic aromatic phenyl and indole moieties results in development of an aptamer binding human insulin receptor with sub-nanomolar affinity and exquisite specificity. Cryo-EM structure reveals the importance of each aromatic modification, either in stabilizing the secondary structure or facilitating interactions with the protein surface. This approach addresses the main drawbacks of aptamer selection and has potential for high-throughput screening and accelerating the development of next-generation aptamers for diagnostics or therapeutics.</p></div>

New technology streamlines the development of aptamers, synthetic alternatives to antibodies

<p><strong>Clarity 10.2 expands instrument control capabilities with new control modules and updates the MS extension to help you work more efficiently.</strong></p><h4><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity</strong></a><strong> 10.2 highlights</strong></h4><ul><li>New and updated control modules</li><li>Improved MS data import and export</li><li>Obsolete hardware support ended</li></ul><h4><strong>Instrument control modules</strong></h4><p>Clarity 10.2 introduces new instrument control modules from Annuo (AS-3117, FAS-3823) and updated instrument controls form Sykam and Ecom.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Instrument_control_modules_5de26782b0.jpg" alt="DataApex: Instrument control modules" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Instrument_control_modules_5de26782b0.jpg 228w," sizes="100vw" width="380" height="260"></p><h4><strong>MS data import/export improvements</strong></h4><p>Clarity improves MS data exchange, especially for *.cdf files. MS instruments now support export and import of multiple spectral data and non-spectral signal data in the same CDF file. Import also better handles uniform sampling information, m/z Step values, scale factors, and file names with non-ASCII characters. Exporting individual chromatogram signals from MS instruments is now available through a separate Export Chromatogram dialog.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_MS_data_import_export_improvements_a7967a4020.jpg" alt="DataApex: MS data import-export improvements" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_MS_data_import_export_improvements_a7967a4020.jpg 228w," sizes="100vw" width="378" height="259"></p><h4><strong>Obsolete hardware support terminated</strong></h4><p>Due to changes in Windows driver security requirements, this update discontinues support for obsolete hardware, including INT7, INT9, U-PAD, U-PAD2, and CB20.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Obsolete_hardware_support_terminated_24d9329419.jpg" alt="DataApex: Obsolete hardware support terminated" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Obsolete_hardware_support_terminated_24d9329419.jpg 228w," sizes="100vw" width="378" height="259"></p><blockquote><p><strong>Explore the complete list of all changes, fixes, and additions in version 10.2.</strong></p><p><strong>👉</strong><a target="_blank" rel="noopener noreferrer" href="https://www.dataapex.com/version_history?product=1"><strong>See the complete changelog&nbsp;</strong></a></p></blockquote>

Clarity Chromatography Software 10.2 released!

<p><strong>🎤Dr. Leigh Terry (University of Alabama)</strong></p><p><strong>In this episode of Concentrating on Chromatography, we sit down with Dr. Leigh Terry from the University of Alabama to explore one of the biggest challenges in environmental analysis today: understanding—and accurately measuring—PFAS in water systems.</strong></p><p>While most regulatory methods focus on a small number of compounds like PFOA and PFOS, there may be thousands of PFAS compounds in the environment—and much of that burden goes undetected.</p><h4><strong>In this episode, we cover:</strong></h4><ul><li>Why PFAS are called “forever chemicals” (and why that label is evolving)</li><li>The limitations of targeted<strong> LC-MS/MS methods</strong></li><li>What the fluorine mass balance problem reveals about PFAS destruction</li><li>How combustion ion chromatography (<strong>CIC</strong>) helps measure total organofluorine</li><li>Why “99.99% removal” doesn’t always mean what you think</li><li>Where PFAS actually end up in wastewater treatment systems</li><li>The most effective technologies for PFAS removal today</li><li>Why drinking water may only account for ~20% of total PFAS exposure</li></ul><h4><strong>Key Insight:</strong></h4><p>Even when analyzing dozens of PFAS compounds, researchers may only be capturing a small fraction of total organic fluorine—raising major questions about how we monitor and regulate these contaminants.</p><h3><strong>Video Transcription</strong></h3><p>In this episode of <i>Concentrating on Chromatography</i>, Dr. Leigh Terry discusses PFAS contamination in drinking water, the analytical challenges associated with measuring these compounds, current treatment technologies, and future directions for monitoring and regulation. The conversation highlights how analytical chemistry, environmental engineering, and public health intersect in addressing one of today's most discussed classes of emerging contaminants.</p><h4><strong>Understanding PFAS and Their Significance</strong></h4><h5><strong>The University of Alabama Water Quality Research Center</strong></h5><p>Dr. Leigh Terry is part of the University of Alabama's Center for Water Quality Research. The center operates an analytical laboratory focused on drinking water quality and the detection of contaminants at extremely low concentrations.</p><p>The laboratory specializes in:</p><ul><li>Drinking water analysis</li><li>Organic contaminants</li><li>Emerging contaminants</li><li>PFAS monitoring</li><li>Water quality research</li></ul><p>Their work supports both research initiatives and practical solutions for water utilities and environmental agencies.</p><h4><strong>Why Focus on PFAS?</strong></h4><p>Although PFAS compounds have existed since the 1940s, public awareness has increased dramatically only in recent years.</p><p>According to Dr. Terry, several factors contributed to the rapid growth of PFAS research:</p><ul><li>Increased media attention</li><li>New regulatory initiatives</li><li>Growing evidence of human exposure</li><li>Expanding research opportunities</li><li>Greater understanding of potential health risks</li></ul><p>PFAS are not new contaminants. Rather, society is only beginning to understand their prevalence in the environment and their potential impacts on human health.</p><h4><strong>The Development of Standardized PFAS Methods</strong></h4><p>One major advancement in PFAS analysis has been the development of standardized EPA methods.</p><p>These methods allow:</p><ul><li>Consistent testing procedures</li><li>Comparable results between laboratories</li><li>Regulatory monitoring</li><li>Reliable data interpretation</li></ul><p>Dr. Terry notes that many of these standardized approaches began appearing around 2018–2019, providing a common framework for analytical laboratories and researchers.</p><h4><strong>How Large Is the PFAS Universe?</strong></h4><p>Many people are familiar with PFOA and PFOS, two of the most heavily studied PFAS compounds. However, these represent only a small fraction of the broader PFAS family.</p><p>PFOA and PFOS are often referred to as:</p><ul><li>Legacy PFAS compounds</li><li>Original PFAS contaminants</li><li>Early commercial PFAS chemicals</li></ul><p>The challenge is that even minor modifications to molecular structure create entirely new PFAS compounds.</p><p>Researchers estimate:</p><ul><li>Thousands of PFAS compounds exist</li><li>Some estimates exceed 10,000 compounds</li><li>Exact numbers depend on how PFAS are defined</li></ul><p>Scientific debate continues regarding classification and definition, making precise counting difficult.</p><h4><strong>Why PFAS Are Called "Forever Chemicals"</strong></h4><p>Dr. Terry notes that the phrase "forever chemicals" has become widely used, although she suggests the terminology could benefit from rebranding.</p><p>PFAS persistence results from two key chemical properties.</p><h5><strong>1. Amphiphilic Structure</strong></h5><p>PFAS molecules contain:</p><ul><li>A water-loving (hydrophilic) head group</li><li>A water-repelling (hydrophobic) fluorinated tail</li></ul><p>This unusual combination allows PFAS to partition between:</p><ul><li>Water</li><li>Solids</li><li>Air-water interfaces</li><li>Foam</li></ul><p>Unlike many organic compounds, PFAS can interact effectively with multiple environmental phases.</p><h5><strong>2. Extremely Strong Carbon–Fluorine Bonds</strong></h5><p>The carbon–fluorine bond is among the strongest bonds in organic chemistry.</p><p>As Dr. Terry explains:</p><ul><li>Large amounts of energy are required to break these bonds</li><li>Natural degradation processes are often ineffective</li><li>Destruction can require highly aggressive treatment conditions</li></ul><p>These properties make PFAS extremely persistent in both environmental systems and biological organisms.</p><h4><strong>Toxicity, Regulations, and Environmental Behavior</strong></h4><h5><strong>Understanding PFAS Toxicity</strong></h5><p>One of the biggest challenges in PFAS regulation is the incomplete understanding of toxicity.</p><p>Dr. Terry explains that EPA regulations generally consider three factors:</p><ul><li>Presence in drinking water sources</li><li>Toxicity to humans</li><li>Availability of practical treatment options</li></ul><p>While some PFAS compounds are known to be harmful, many others remain insufficiently studied. Furthermore, PFAS often occur as mixtures rather than individual compounds.</p><p>This creates important scientific questions:</p><ul><li>What is the toxicity of individual PFAS?</li><li>What is the toxicity of PFAS mixtures?</li><li>How should cumulative exposure be evaluated?</li></ul><p>These uncertainties continue to drive active research.</p><h4><strong>What Happens to PFAS in Wastewater Treatment Plants?</strong></h4><p>PFAS do not behave like many conventional contaminants.</p><p>Rather than remaining fully dissolved in water, they often accumulate at interfaces such as:</p><ul><li>Water-solid interfaces</li><li>Water-air interfaces</li><li>Foam layers</li><li>Biological solids</li></ul><p>As a result:</p><ul><li>Some PFAS accumulate in biosolids</li><li>Some partition into foam</li><li>Some remain in treated effluent</li></ul><p>Their distribution depends on wastewater composition and treatment processes.</p><h4><strong>Regulatory Monitoring and Targeted LC-MS Analysis</strong></h4><p>Current EPA regulations focus on targeted analysis of specific PFAS compounds.</p><p>Examples include:</p><ul><li>PFOA</li><li>PFOS</li></ul><p>Drinking water regulations currently establish maximum contaminant levels (MCLs) for these compounds at extremely low concentrations.</p><p>Advantages of targeted LC-MS analysis include:</p><ul><li>Clearly defined analytes</li><li>Established regulatory limits</li><li>High analytical sensitivity</li><li>Reliable quantitation</li></ul><p>However, limitations remain:</p><ul><li>Only a small subset of PFAS is measured</li><li>Many PFAS compounds remain undetected</li><li>Total PFAS burden may be underestimated</li></ul><p>As Dr. Terry notes, targeted analysis provides only part of the overall picture.</p><h4><strong>The Fluorine Mass Balance Problem</strong></h4><p>One of the most important concepts discussed in the interview is fluorine mass balance.</p><p>When PFAS degrade, fluorinated fragments may remain in the environment.</p><p>This creates a critical question:</p><p>Are treatment technologies truly destroying PFAS, or merely transforming them into shorter-chain PFAS compounds?</p><p>To answer this, researchers perform fluorine mass balance calculations using:</p><ul><li>Targeted PFAS analysis</li><li>Fluoride measurements</li><li>Total organic fluorine measurements</li></ul><p>A successful destruction process should ultimately convert PFAS into fluoride ions rather than simply producing smaller PFAS molecules.</p><h4><strong>Advanced Analysis, Treatment Technologies, and Future Directions</strong></h4><h5><strong>Combining Targeted and Bulk Fluorine Measurements</strong></h5><p>Dr. Terry's group complements targeted LC-MS analysis with measurements of total organic fluorine.</p><p>Approaches include:</p><ul><li>Absorbable Organic Fluorine (AOF)</li><li>Extractable Organic Fluorine (EOF)</li><li>Combustion Ion Chromatography (CIC)</li></ul><p>In these methods:</p><ul><li>Organic fluorine is captured</li><li>Samples are combusted</li><li>Released fluoride is quantified</li></ul><p>This provides insight into total fluorinated content, although contributions may originate from sources beyond PFAS, including pharmaceuticals and consumer products.</p><h4><strong>Surprising Findings from Combined Analysis</strong></h4><p>One important finding from wastewater studies was that targeted PFAS measurements accounted for only a small fraction of total organic fluorine.</p><p>Dr. Terry reports that:</p><ul><li>Approximately 4% of measured AOF could be explained by targeted PFAS compounds</li><li>The majority of organic fluorine remained unidentified</li></ul><p>This suggests that environmental fluorine chemistry is considerably more complex than currently represented by routine monitoring programs.</p><h4><strong>Preventing PFAS Contamination in the Laboratory</strong></h4><p>PFAS analysis requires exceptionally strict quality control.</p><p>Dr. Terry's laboratory routinely:</p><ul><li>Tests every new batch of SPE cartridges</li><li>Tests carbon tubes before use</li><li>Uses DI water blanks</li><li>Verifies consumables labeled as PFAS-free</li><li>Collects field blanks</li><li>Monitors analytical blanks throughout workflows</li></ul><p>These practices help prevent contamination from laboratory materials and consumables, a common challenge in ultra-trace PFAS analysis.</p><h4><strong>Current PFAS Treatment Technologies</strong></h4><p>Three technologies currently dominate PFAS removal in drinking water treatment:</p><ul><li>Granular Activated Carbon (GAC)</li><li>Ion Exchange Resins</li><li>Reverse Osmosis (RO)</li></ul><p>Selection depends on:</p><ul><li>PFAS concentration</li><li>Water quality</li><li>Local operating conditions</li><li>Utility infrastructure</li></ul><p>Although many emerging technologies are being investigated, these remain the most widely implemented solutions.</p><h4><strong>Membrane Filtration and Pretreatment</strong></h4><p>Dr. Terry collaborates with colleagues studying membrane-based PFAS treatment.</p><p>Her own work focuses on pretreatment through biological filtration.</p><p>The strategy involves:</p><ul><li>Removing natural organic matter</li><li>Reducing membrane fouling</li><li>Improving membrane performance</li><li>Extending operational efficiency</li></ul><p>This integrated approach demonstrates how multiple treatment technologies can work together to improve PFAS removal.</p><h4><strong>Regional Monitoring Projects</strong></h4><p>The University of Alabama team participates in EPA-supported monitoring efforts along the Gulf Coast.</p><p>Their observations indicate:</p><ul><li>PFAS rarely occur alone</li><li>Multiple PFAS compounds frequently co-occur</li><li>Contamination often originates from identifiable point sources</li></ul><p>Examples include:</p><ul><li>Industrial facilities</li><li>Manufacturing operations</li><li>Military installations</li><li>Carpet manufacturing facilities</li></ul><p>Source identification remains a critical component of environmental monitoring programs.</p><h4><strong>Future Directions for PFAS Monitoring</strong></h4><p>Looking ahead, Dr. Terry sees several opportunities for improvement.</p><p>Desired advances include:</p><ul><li>In situ monitoring technologies</li><li>Portable detection systems</li><li>Reduced analytical complexity</li><li>Lower instrument costs</li><li>Less expensive consumables</li><li>Faster analysis workflows</li></ul><p>Current PFAS testing requires substantial expertise, specialized instrumentation, and rigorous quality control, making widespread implementation challenging.</p><h4><strong>Dr. Terry's Perspective on Long-Term Solutions</strong></h4><p>When asked what major PFAS challenge she would most like to solve, Dr. Terry offered a broader perspective.</p><p>Rather than focusing solely on remediation, she emphasized prevention.</p><p>Her view is that society should:</p><ul><li>Better evaluate chemical toxicity before commercialization</li><li>Assess risks before large-scale deployment</li><li>Reduce introduction of harmful compounds into the environment</li><li>Support utilities tasked with contaminant removal</li></ul><p>She notes that water utilities often bear the responsibility of removing contaminants they did not create, highlighting the need for broader societal and regulatory support.</p><h4><strong>Final Thoughts</strong></h4><p>Dr. Terry encourages consumers to:</p><ul><li>Learn where their drinking water originates</li><li>Read annual water quality reports</li><li>Stay informed about local water quality</li><li>Consider appropriate home filtration where needed</li></ul><p>At the same time, she emphasizes confidence in municipal water systems and the importance of continued investment in water quality research, monitoring, and treatment technologies.</p><h4><strong>Conclusion</strong></h4><p>PFAS remain one of the most complex challenges in environmental chemistry and water treatment. Through advanced analytical methods such as LC-MS/MS, combustion ion chromatography, fluorine mass balance approaches, and large-scale monitoring programs, researchers like Dr. Leigh Terry are helping improve our understanding of these persistent contaminants.</p><p>The interview highlights that solving the PFAS challenge will require a combination of better analytical tools, improved treatment technologies, stronger regulatory frameworks, and a greater emphasis on prevention before contaminants enter the environment.</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>

PFAS in Water: Why We’re Missing 96% of the Problem

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Since 1991 DataApex develops and manufactures chromatography data stations. DataApex is constantly striving to provide users with efficient and up-to-date tools for chromatography data processing.

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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.

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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>

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