<p><strong>Taťána Gazárková is currently a&nbsp;postdoctoral fellow in the Laboratory of Antibiotic Resistance and Microbial Metabolomics. During her doctoral studies, she focused on chromatography and mass spectrometry. Recently, she was awarded second place in the “Sanofi Prize for Pharmacy 2026” competition.</strong></p><p><strong>Taťána Gazárková </strong>is currently a&nbsp;postdoctoral fellow in the <strong>Laboratory of Antibiotic Resistance and Microbial Metabolomics</strong>. During her doctoral studies, she focused on chromatography and mass spectrometry. Recently, she was awarded second place in the <strong>“Sanofi Prize for Pharmacy 2026” </strong>competition, which is awarded by the<strong> French Embassy in the Czech Republic</strong> for her dissertation – Steroid Analysis Using Modern Chromatographic and Mass Spectrometry Techniques: From Fundamental Studies to Targeted Bioanalytical Applications (supervisor: <strong>Lucie Nováková, Charles University</strong>).&nbsp;</p><h5><strong>What makes this field particularly exciting or unique in your view?</strong></h5><p>What I&nbsp;enjoy about analytical chemistry is that, to a&nbsp;certain extent, it is a&nbsp;kind of detective work. You are often looking for ways to “make the invisible visible”. In other words, extract the information you are interested in from a&nbsp;complex sample and then interpret it correctly. What also appeals to me about bioanalytical chemistry is its interdisciplinary nature. It brings together analytical chemistry, biochemistry, biology and medicine, which means that you need to be able not only to translate a&nbsp;biological or clinical question into a&nbsp;measurable analytical experiment, but also to place the resulting data back into a&nbsp;broader biological context. This combination of different perspectives is probably what I&nbsp;enjoy most about the field. At the same time, there is still plenty of room for fundamental research, ranging from studying analytical techniques themselves and improving them to developing new methodological approaches.</p><h5><strong>How did you end up at the </strong><a target="_blank" rel="noopener noreferrer" href="https://mbu.cas.cz/en/research/laboratory-of-antibiotic-resistance-and-microbial-metabolomics"><strong>Laboratory of Antibiotic Resistance and Microbial Metabolomics</strong></a><strong>, and what project are you currently working on?</strong></h5><p>I came to the Institute of Microbiology through a&nbsp;joint project between<strong> Dr Zdeněk Kameník and Assoc. Prof. Jan Bobek from the First Faculty of Medicine, Charles University</strong>. For me, it was also an opportunity to move from targeted analysis and the study of chromatographic techniques towards untargeted metabolomics and new biological questions.</p><p>In the project, we are trying to identify new biologically active compounds that would be effective, particularly against pathogenic fungi. As a&nbsp;potential source of such compounds, we study streptomycetes, bacteria known for their ability to produce a&nbsp;wide range of biologically active compounds, including many antibiotics that are currently in clinical use. We focus on less-explored host-associated streptomycetes, in which we had already observed antifungal activity in previous experiments. We are especially interested in strains active against Candida albicans whose activity cannot be explained by the presence of a&nbsp;known bioactive compound. These strains may represent an interesting source of novel compounds. We then integrate the results of untargeted metabolomic analyses with genomic analyses, which allows us to obtain a&nbsp;more comprehensive view of the biosynthetic potential of selected strains.</p><h5><strong>You also took part in this year’s Vědafest, a&nbsp;science outreach event for the public. What was it like?</strong></h5><p>I already had some experience with science outreach through events such as Researchers’ Night and the Science Fair at my previous institution, but this year’s Vědafest was still new to me in some ways. This time, I&nbsp;was presenting a&nbsp;field that I&nbsp;myself had entered only relatively recently. It was therefore more challenging to find the right analogies and explain the essence of the topic in a&nbsp;way that was simple, yet precise and scientifically accurate. At the same time, that was exactly what made it inspiring. It forces you to look at your own work from a&nbsp;different perspective. What I&nbsp;enjoyed most was the spontaneity and curiosity of the children, who often came up with questions that would never even occur to an adult.</p><h5><strong>What are the biggest challenges you face on your scientific journey, and what helps you overcome them?</strong></h5><p>One of the greatest, but at the same time most interesting, challenges is, in my view, the uncertainty that is inseparably linked to research. For a&nbsp;long time, you often do not know whether you have taken the right direction in addressing a&nbsp;particular question or whether you will ultimately manage to find that figurative final piece of the puzzle. At the same time, this uncertainty is precisely what makes science exciting for me.</p><p>Another major challenge, particularly in interdisciplinary projects, is communication. It is important from the very formulation of a&nbsp;hypothesis and the planning of experiments through to the interpretation of results, including negative ones, and placing them in a&nbsp;broader context. To some extent, every field has its own language, and finding a&nbsp;common understanding is not always straightforward. Personally, I&nbsp;find it very helpful to be able to discuss problems with colleagues on an ongoing basis, whether individually or during regular laboratory seminars. One of the major strengths of our current group is its interdisciplinary nature, which allows me to look at the same problem from several different perspectives. It is also important for me not to lose my curiosity, because that is ultimately what leads us to ask further questions.</p><h5><strong>What are your plans after completing your PhD?</strong></h5><p>After finishing my PhD, I&nbsp;decided that I&nbsp;do not need to have everything that comes next precisely mapped out straight away. I&nbsp;would like to keep different options open for a&nbsp;while and continue building on my experience in analytical chemistry, while at the same time connecting it with other areas that have a&nbsp;biological or medical relevance. I&nbsp;believe that we can keep learning throughout our lives, so I&nbsp;am quite curious to see where the next stage of my journey will take me.</p><p><i>Thank you for the interview!</i></p>

Interview: What Drew Postdoc Taťána Gazárková to Analytical Chemistry

<p><strong>Per- and polyfluoroalkyl substances (PFAS) have earned the moniker "forever chemicals" due to their extreme persistence in the environment. Their detection is crucial for protecting public health and the environment as these synthetic compounds continue to pose significant challenges worldwide. This comprehensive exploration examines why PFAS detection matters, current detection methods, and future directions in addressing PFAS contamination.</strong></p><h3><strong>Understanding PFAS and Their Health Impacts</strong></h3><p>PFAS are a class of synthetic organic compounds with diverse structures, properties, and uses. Despite their diversity, all PFAS contain perfluoroalkyl moieties that are extremely resistant to environmental and metabolic degradation [1]. This high persistence is a defining characteristic that makes PFAS management particularly challenging.</p><h3><strong>Documented Health Effects</strong></h3><p>Current scientific research has linked PFAS exposure to numerous adverse health outcomes:</p><ul><li>Reproductive effects including decreased fertility and increased high blood pressure in pregnant women [8]</li><li>Developmental effects in children such as low birth weight, accelerated puberty, and behavioral changes [8]</li><li>Reduced immune system function, including decreased vaccine response</li><li>Interference with natural hormones and endocrine disruption</li><li>Increased cholesterol levels and obesity risk</li><li>Increased risk of several cancers, including prostate, kidney, testicular, oral cavity/pharynx, brain, and endocrine cancers [3]</li></ul><p>A 2023 study linked PFAS-contaminated water with up to a <strong>33% increase in cancer incidence</strong> in affected areas [3]. The study compared regions with elevated PFAS levels to cancer data from the National Cancer Institute, finding higher incidences of various cancers after controlling for factors like smoking and obesity.</p><h3><strong>Environmental Persistence and Contamination</strong></h3><p>The extreme persistence of PFAS represents a fundamental concern for environmental management. PFAS are considered the most environmentally persistent substances among organic chemicals [7]. This persistence means that even if all PFAS uses were immediately phased out, existing contamination would continue to affect ecosystems and water supplies for generations.</p><p>A 2023 study at a military fire training site estimated that PFAS contamination will persist for centuries without remediation [7]. The research found that terminal PFAS still exceed regulatory limits by 2000-fold decades after aqueous film-forming foam (AFFF) use ceased, with precursors accounting for around half of the extractable organofluorine across years.</p><h3><strong>Current Detection Methods</strong></h3><h4><strong>EPA Standardized Methods</strong></h4><p>The<strong> Environmental Protection Agency (EPA</strong>) has developed several standardized methods for PFAS detection, each with specific applications and capabilities:</p><h5><strong>EPA Method 533</strong></h5><p><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/epa-533-drying-down-pfas-samples-after-spe"><strong>EPA Method 533</strong></a> focuses on "short chain" PFAS with carbon chain lengths of<strong> C4 to C12</strong>. Released in December 2019, this method complements Method 537.1 and includes several key features:</p><ul><li>Uses isotope dilution quantification approach with extracted internal standards, which reduces overall analytical uncertainty</li><li>Employs weak anion exchange solid phase extraction cartridges as opposed to polystyrene divinylbenzene used in 537.1</li><li>Can analyze 25 PFAS compounds, including additional short-chain PFAS that were not apart of Method 537.1</li><li>Allows for longer holding times: 28 days to extraction and 28 days to analyze (compared to 14 days to extraction in Method 537.1)</li><li>Uses ammonium acetate as a preservative (versus Trisma in Method 537.1) [1]</li></ul><h5><strong>EPA Method 537/537.1</strong></h5><p><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/sample-concentration-epa-method-537-pfas-determination"><strong>EPA Method 537 </strong></a>was first published in 2009 for the determination of 14 PFAS in drinking water [6]. It was later updated to Method 537.1 in 2018 (with editorial updates in 2020) to expand its capabilities:</p><ul><li>Uses<a target="_blank" rel="noopener noreferrer" href="https://www.organomation.com/what-is-solid-phase-extraction-spe"><strong> solid phase extraction (SPE) </strong></a>and<a target="_blank" rel="noopener noreferrer" href="https://www.organomation.com/preparing-samples-for-lc-ms/ms-analysis"><strong> liquid chromatography/tandem mass spectrometry (LC-MS/MS)</strong></a></li><li>Method 537.1 expanded detection to 18 PFAS compounds, including HFPO-DA (one component of GenX technology)</li><li>Utilizes styrene-divinylbenzene (SDVB) media for extraction</li><li>Requires samples to be extracted within 14 days and analyzed within 28 days</li><li>Methanol is used to elute the extracts. This should then be reconstituted with a 96:4 methanol:water mixture [1]</li></ul><p>Together, Methods 533 and 537.1 can detect a total of <strong>29 unique PFAS compounds in drinking water </strong>and are approved for monitoring under the fifth Unregulated Contaminant Monitoring Rule (UCMR 5) and the PFAS National Primary Drinking Water Regulation [1] [3].</p><h5><strong>EPA Method 1633</strong></h5><p><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/preparing-diverse-sample-matrices-for-epa-method-1633"><strong>EPA Method 1633</strong></a>, released in 2024, represents a significant advancement in PFAS analysis:</p><ul><li>Developed for the analysis of <strong>40 PFAS compounds </strong>in various matrices, including surface water, groundwater, wastewater, soil, biosolids, sediment, landfill leachate, and fish tissue</li><li>Expands beyond the drinking water focus of Methods 533 and 537.1</li><li>Provides a standardized approach that may replace modified drinking water methods (i.e., modified EPA 537) that were previously used for non-drinking water matrices [1]</li></ul><h4><strong>Conventional Analytical Techniques</strong></h4><p>The gold standard for PFAS analysis involves chromatographic techniques coupled with mass spectrometry:</p><ul><li>Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) is the most widely used method for PFAS analysis, offering high sensitivity and specificity [1]</li><li>High-Resolution Mass Spectrometry (HRMS) allows for rapid detection and identification of PFAS species at very low concentrations [5]</li></ul><p>These techniques can detect PFAS at parts per trillion (ppt) levels, which is essential given the low concentrations at which PFAS can cause health effects [1]. However, these methods require sophisticated equipment, specialized training, and significant financial resources, making them inaccessible in many regions, particularly in developing countries.</p><h4><strong>Emerging Detection Technologies</strong></h4><p>Several innovative approaches are being developed to address the limitations of conventional methods:</p><ul><li>Electrochemical biosensors using modified electrodes have shown promise for selective PFAS detection with low detection limits [2]</li><li>Surface-Enhanced Raman Spectroscopy (SERS) uses metallic nanoparticles and can be made into a portable method for on-site testing [1]</li><li>Molecular imprinted polymers (MIPs) offer thermal and physical stability, reusability, and low-cost synthesis for PFAS detection [6]</li></ul><p>These emerging technologies aim to provide more accessible, field-deployable, and cost-effective alternatives to traditional laboratory-based methods.</p><h3><strong>Challenges in PFAS Detection</strong></h3><h4><strong>Analytical Challenges</strong></h4><p>Detecting PFAS presents several technical challenges:</p><ul><li>The ubiquity of PFAS in laboratory equipment and accessories can lead to background contamination when measuring at parts-per-trillion levels [1]</li><li>Many components in liquid chromatographs, mass spectrometers, and solid-phase extraction systems contain materials that can leach PFAS compounds [9]</li><li>The vast number of PFAS (thousands of compounds) makes comprehensive detection difficult, as analytical standards are only available for a small subset [1]</li><li>Complex matrices like food and environmental samples require sophisticated sample preparation techniques</li></ul><h4><strong>Global Disparities in Detection Capabilities</strong></h4><p>Access to PFAS detection technology varies significantly worldwide:</p><ul><li>Many developing regions, particularly in Africa, lack adequately equipped laboratories with the necessary instrumentation to detect and measure PFAS</li><li>There is often a scarcity of qualified professionals with experience in PFAS analysis in these regions</li><li>The high cost of acquiring and maintaining sophisticated analytical instruments presents a substantial obstacle to conducting extensive PFAS investigations in resource-limited settings [1]</li><li>Competing priorities such as infectious diseases, poverty, and food security often divert attention and resources from environmental pollutants like PFAS</li></ul><h4><strong>Regulatory Landscape and Compliance</strong></h4><p>The regulatory framework for PFAS is evolving rapidly worldwide:</p><ul><li>The EPA finalized Section 8(a)(7) of the Toxic Substances Control Act in September 2024, requiring manufacturers and importers to report on their use of PFAS since 2011 [10]</li><li>Electronic reporting for PFAS will open on July 11, 2025, with final reporting deadlines in 2026</li><li>Companies must report detailed information including chemical identity, production volumes, industrial and consumer products, worker exposure, and disposal methods [10]</li></ul><p>These regulations are driving demand for more effective and accessible PFAS detection methods to ensure compliance and protect public health.</p><h3><strong>Future Directions in PFAS Detection</strong></h3><h4><strong>Technological Advancements</strong></h4><p>The future of PFAS detection lies in developing more accessible, sensitive, and comprehensive methods:</p><ul><li>Non-targeted screening methods that can identify unknown PFAS compounds without requiring analytical standards for each specific compound</li><li>Total fluorine analysis techniques like Adsorbable Organic Fluorine and Total Oxidizable Precursor Assay that can quantify the presence of fluorine atoms within a sample [1]</li><li>Portable sensors and field-deployable technologies that enable on-site monitoring and rapid response to contamination events</li><li>AI-driven solutions that can improve data analysis and interpretation for complex PFAS mixtures</li></ul><h4><strong>Collaborative Approaches</strong></h4><p>Addressing the global challenge of PFAS detection requires coordinated efforts:</p><ul><li>International partnerships between researchers in developed and developing regions to enhance expertise and capacity building</li><li>Standardization of analytical methods to ensure consistency and comparability of results across different laboratories and regions</li><li>Open data sharing and collaboration across countries to leverage collective knowledge and resources</li><li>Integration of PFAS monitoring into broader environmental and public health surveillance systems</li></ul><h3><strong>Conclusion</strong></h3><p>The detection of PFAS is not merely a technical challenge but a critical public health and environmental imperative [1]. As these "forever chemicals" continue to persist in our environment, developing effective, accessible, and comprehensive detection methods becomes increasingly important. By advancing detection technologies, strengthening regulatory frameworks, and fostering global collaboration, we can better understand, monitor, and ultimately mitigate the impacts of PFAS contamination.</p><p>The EPA's standardized methods (533, 537.1, and 1633) provide crucial tools for monitoring PFAS in various environmental matrices, but continued innovation is needed to address the full spectrum of PFAS compounds and to make detection more accessible globally [1] [6]. The path forward requires sustained investment in research and development, capacity building in resource-limited settings, and a commitment to environmental justice that ensures all communities have access to the tools and information needed to protect themselves from PFAS exposure. Only through such comprehensive approaches can we hope to address the complex challenges posed by these persistent pollutants.</p><p><span>Be sure to check out our other installments of our&nbsp;</span><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/introducing-our-environmental-contaminants-series-making-sense-of-the-alphabet-soup"><span>Environmental Contaminant Series</span></a><span>&nbsp;covering&nbsp;</span><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/the-importance-of-detecting-persistent-organic-pollutants-pops"><span>Persistent Organic Pollutants (POPs)</span></a><span>,&nbsp;</span><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/the-importance-of-detecting-polycyclic-aromatic-hydrocarbons-pahs"><span>Polycyclic Aromatic Hydrocarbons (PAHs)</span></a><span>,&nbsp;</span><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/the-importance-of-detecting-semi-volatile-organic-compounds-svocs"><span>Semi-Volatile Organic Compounds (SVOCs)</span></a><span>, and </span><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/the-importance-of-detecting-polychlorinated-biphenyls-pcbs"><span>Polychlorinated Biphenyls (PCBs)</span></a><span>.</span></p>

The Importance of Detecting Per- and Polyfluoroalkyl Substances (PFAS)

News from LabRulezLCMS Library - Week 36, 2026

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The Czech Academy of Sciences (CAS) was established by Act No. 283/1992 Coll. as the Czech successor of the former Czechoslovak Academy of Sciences. It is set up as a complex of 54 public research institutions.

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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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