<div><p><strong>Mulching films used in agriculture gradually break down and can become a significant source of microplastics in soils. A new study shows that these particles affect not only soil structure but also microbial life and nitrogen cycling.</strong></p><p><i>“We wanted to understand how microplastics from both conventional and biodegradable mulching films influence soil properties, microbial diversity and functions in real conditions,”</i> explains <strong>Klára Šmídová</strong>, the study’s co-author . <i>“That’s why we added realistic amounts of microplastics to soils in experimental plots in Finland, Germany, and Spain, monitored them over two growing seasons, and compared them with the control plots.”</i></p><p>The results revealed that microplastics alter soil characteristics and microbial communities, although not always in the same way. <i>“ However, a consistent finding was the decline in microbial activity associated with key processes, including nitrogen cycling, with negative effects increasing at higher microplastic concentrations and becoming more pronounced in the second year,” </i>Šmídová adds. Because the microplastic levels used in the study reflect amounts already found in European soils, the findings highlight real risks to soil health. <i>“We also found that the effects were stronger in southern than in northern Europe, likely due to differences in climate and soil conditions. This means that protecting soils from plastic pollution will require region-specific risk assessments,”</i> she says.</p><p>Over 60% of European soils are estimated to be unhealthy, with ongoing degradation driven by unsustainable land use, contamination, climate change, and extreme weather events. In response, the EU Parliament adopted the Soil Monitoring Law in October 2025, aiming to achieve healthy soils across Europe by 2050. <i>“The law highlights the role of soil health in food security, water quality, and climate objectives, and establishes consistent soil monitoring across Member States. It includes measures to support farmers and foresters, while also creating a public list of potentially contaminated sites and an indicative watch list of emerging soil contaminants,” </i>explains Klára Šmídová.</p><p>The project brought together 19 research groups across Europe. <i>“After each season, hundreds of samples were colle cted and sent to partners for analysis. This paper focuses on soil properties, microbial diversity, and greenhouse gas emissions. Two more manuscripts—on plastic additives and microplastic fate, and on soil invertebrates—are in preparation. Together, they will give us a complete picture of how agricultural microplastics affect soil ecosystems,” </i>concludes Klára Šmídová.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/RECETOX_Vysledky_nove_studie_ukazaly_ze_mikroplasty_meni_vlastnosti_pudy_a_mikrobialni_spolecenstva_i_v_realnych_podminkach_6ee3413a7b.jpg" alt="RECETOX: New Study Reveals How Agricultural Plastics Impact Soil Health In Real Conditions" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_RECETOX_Vysledky_nove_studie_ukazaly_ze_mikroplasty_meni_vlastnosti_pudy_a_mikrobialni_spolecenstva_i_v_realnych_podminkach_6ee3413a7b.jpg 171w," sizes="100vw" width="738" height="674"></p><blockquote><h4><strong>The Original article</strong></h4><h4><a target="_blank" rel="noopener noreferrer" href="https://www.sciencedirect.com/science/article/pii/S0269749125015866?via%3Dihub#sec2"><span><strong>Conventional and biodegradable agricultural microplastics: effects on soil properties and microbial functions across a European pedoclimatic gradient</strong></span></a></h4><p>Šmídová K., Soinne H., Kim S. W., Tirronniemi J., Meffe R., Redondo-Hasselerharm P. E., Braun M., Rillig M. C., Fritze H., Adamczyk B., Nikama J., Kaseva J., Saartama V., Amelung W., Hurley R., Hofman J., Nizzetto L., Selonen S., Velmala S.</p><p>Environ. Pollut. 386 (2025) 127212</p><p><a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1016/j.envpol.2025.127212">10.1016/j.envpol.2025.127212</a></p><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6></blockquote><h4><strong>Abstract</strong></h4><div><p>Agricultural plastics like mulching films may become a major source of microplastic (MP) soil contamination during their degradation and fragmentation. This study investigates the effects of agricultural MPs from conventional (linear low-density polyethylene, PE) and biodegradable (starch-blended polybutylene adipate co-terephthalate, PBAT-BD) mulching films on soil physicochemical properties, aggregation, microbial diversity and functions, litter decomposition, and greenhouse gases emissions (GHG). For this purpose, MPs were mixed into soils at realistic MP concentrations of 0.005&nbsp;% and 0.05&nbsp;% (w/w) in 2022 on experimental plots in three EU countries representing different pedoclimatic conditions (Finland, Germany and Spain), followed by monitoring of the above-mentioned variables in the subsequent growing seasons 2022 and 2023. We found several significant MP-induced effects for soil properties, aggregation, microbial diversity, litter decomposition, and GHG, but the effect endpoints were less pronounced or varied considerably. Contrarily, microbial activity, contributing to soil functions such as nitrogen cycling, was consistently reduced by both conventional and biodegradable MPs. The reductions were more pronounced after the second season and for the higher MP treatment. As the higher MP concentration (i.e., 0.05&nbsp;% w/w) is environmentally relevant in Europe, our findings emphasize the potential effects of environmentally relevant MP concentrations on soil health. Furthermore, the effects increased from north to south, probably modulated by varying pedoclimatic conditions, inducing reflection of a need for regionally tailored risk</p></div></div>

New Study Reveals How Agricultural Plastics Impact Soil Health In Real Conditions

<h3><strong>Charged for Action: The Hidden Secrets of AEX Oligonucleotide Analysis</strong></h3><p><strong>Oligonucleotides—short, well-defined fragments of DNA or RNA—have become indispensable tools in modern life sciences. They underpin cutting-edge applications in molecular diagnostics, gene therapy, and pharmaceutical development. Before oligonucleotides can be confidently used in research or clinical settings, however, their quality must be rigorously assessed. Purity, sequence integrity, length distribution, and chemical modifications all play a decisive role in their performance.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_2_45eee54fa0.jpg" alt="KNAUER: Oligos Made Easy - Part 2: AEX" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_2_45eee54fa0.jpg 245w," sizes="100vw" width="1534" height="711"></p><p>Among the analytical techniques available today, <strong>anion exchange chromatography (AEX)</strong> stands out as a robust and highly informative method for characterizing oligonucleotides. By exploiting their intrinsic negative charge, AEX provides detailed insight into product composition and impurity profiles that are difficult to obtain by other approaches.</p><blockquote><p><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6808"><strong>Part 1 of the Oligos series: A Practical Guide to Oligonucleotide Production – From Concept to Final Product</strong></a></p></blockquote><h4><strong>How Scientists Read Oligonucleotides Using Charge</strong></h4><p>At the core of AEX lies a simple but powerful principle: oligonucleotides carry a negatively charged phosphate backbone. This charge increases in a predictable way with strand length and, to a lesser extent, sequence composition. Anion exchange chromatography uses this property to separate oligonucleotides based on differences in charge strength and interaction with a positively charged stationary phase.</p><p>As a result, AEX has become one of the most widely used analytical tools for evaluating oligonucleotide quality. It allows scientists to distinguish full-length products from truncated species, degradation products, or closely related variants—often with single-nucleotide resolution.</p><h4><strong>Why Ion Exchange Works: Binding, Retention, and Release</strong></h4><p>Ion exchange chromatography (IEX) relies on electrostatic interactions between analytes and a charged stationary phase. In the case of oligonucleotides, <strong>anion exchange</strong> is used, where negatively charged molecules interact with positively charged functional groups on the resin—most commonly quaternary amines.</p><p>The system consists of two main components:</p><ul><li><strong>Stationary phase:</strong> A positively charged resin that binds anionic analytes.</li><li><strong>Mobile phase:</strong> An aqueous buffer system, typically combined with a salt gradient, that controls both pH and elution strength.</li></ul><p>Retention in AEX is governed primarily by charge. Molecules with weaker overall charge interact less strongly with the stationary phase and elute earlier, while more highly charged oligonucleotides bind more tightly and require stronger elution conditions.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_1_IEX_overview_including_elution_order_dependency_on_analyte_charge_3419ad3075.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 1 IEX overview including elution order dependency on analyte charge." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_1_IEX_overview_including_elution_order_dependency_on_analyte_charge_3419ad3075.jpg 245w," sizes="100vw" width="1583" height="654"></p><h4><strong>The Five-Step Workflow of Ion Exchange Chromatography</strong></h4><p>AEX separations generally follow a well-established sequence of steps:</p><ol><li><strong>Column equilibration</strong><br>The column is conditioned with the starting buffer until the baseline and pH are stable. This ensures that all charged sites on the resin are ready for interaction.</li><li><strong>Sample loading</strong><br>Samples, prepared in the starting buffer, are introduced under conditions that promote binding of the target oligonucleotides while minimizing retention of unwanted impurities.</li><li><strong>Washing</strong><br>The column is washed with the starting buffer to remove uncharged or weakly interacting components. The baseline stabilizes as these species are flushed away.</li><li><strong>Elution</strong><br>Bound oligonucleotides are released using a salt or pH gradient. Increasing ionic strength introduces competing ions that displace the analytes from the resin. Weakly bound species elute first; strongly charged oligonucleotides elute later.</li><li><strong>Regeneration and re-equilibration</strong><br>A high-salt buffer removes any remaining bound material. The column is then returned to starting conditions in preparation for the next analysis.</li></ol><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_2_Five_steps_of_IEX_procedure_in_blue_outlined_using_an_example_chromatogram_in_red_38dd70b1b1.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 2  Five steps of IEX procedure (in blue), outlined using an example chromatogram (in red)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_2_Five_steps_of_IEX_procedure_in_blue_outlined_using_an_example_chromatogram_in_red_38dd70b1b1.jpg 245w," sizes="100vw" width="1583" height="674"></p><h4><strong>Why AEX Is Especially Effective for Oligonucleotides</strong></h4><p>The repeating phosphate backbone of oligonucleotides gives rise to a strong and uniform anionic character across a wide pH range (typically pH 7–9). This makes oligonucleotides exceptionally well suited for anion exchange separations.</p><p>Key factors influencing AEX behavior include:</p><ul><li><strong>Charge density:</strong> Longer oligonucleotides carry more negative charges and therefore exhibit stronger retention.</li><li><strong>Resin chemistry:</strong> Strong and weak anion exchangers differ in functional groups and pH stability, influencing selectivity and robustness.</li><li><strong>Buffer composition:</strong> The choice of buffering ions and salt gradients directly affects elution strength and resolution.</li></ul><p>Salt gradients—commonly based on chloride ions—compete with the oligonucleotide backbone for binding sites on the resin. By carefully tuning gradient slope and composition, analysts can achieve highly reproducible and finely resolved separations.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_3_Ionic_interactions_and_p_H_influence_on_Anion_Exchange_Chromatography_AEX_612e231ba4.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 3 Ionic interactions and pH influence on Anion Exchange Chromatography (AEX)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_3_Ionic_interactions_and_p_H_influence_on_Anion_Exchange_Chromatography_AEX_612e231ba4.jpg 245w," sizes="100vw" width="1547" height="593"></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_4_AEX_buffer_selection_and_gradient_strategy_chromatogram_with_red_buffer_gradient_curve_53fd1bb11b.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 4 AEX buffer selection and gradient strategy (chromatogram with red buffer gradient curve)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_4_AEX_buffer_selection_and_gradient_strategy_chromatogram_with_red_buffer_gradient_curve_53fd1bb11b.jpg 245w," sizes="100vw" width="1600" height="327"></p><h4><strong>AEX as the Gold Standard for Oligonucleotide Separation</strong></h4><p>Anion exchange chromatography has become the method of choice for both analytical and preparative oligonucleotide workflows. Its advantages include:</p><ul><li><strong>High resolving power:</strong> Closely related impurities, including n–1 or n–2 species, can often be separated and quantified.</li><li><strong>Predictable retention behavior:</strong> In many cases, retention time correlates linearly with oligonucleotide length, simplifying identification.</li><li><strong>Compatibility with modified oligonucleotides:</strong> Even chemically modified sequences retain their anionic nature, allowing AEX to resolve both products and related impurities.</li><li><strong>Excellent control via gradient elution:</strong> Salt gradients provide precise tuning of selectivity and resolution.</li></ul><p>Typically, shorter or degraded oligonucleotides elute at lower ionic strength, while full-length products with higher charge density appear later in the chromatogram.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_5_AEX_Advantages_and_Challenges_7835521e34.jpg" alt="KNAUER: Oligos Made Easy - Part 2 AEX: Figure 5 AEX Advantages and Challenges." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Oligos_Made_Easy_Part_2_AEX_Figure_5_AEX_Advantages_and_Challenges_7835521e34.jpg 245w," sizes="100vw" width="1535" height="707"></p><h4><strong>Final Perspective: Mastering AEX with Confidence</strong></h4><p>Anion exchange chromatography may appear complex at first, but with thoughtful optimization of pH, buffer composition, and gradient conditions, it becomes a highly precise and reliable tool for oligonucleotide analysis. When properly applied, AEX delivers sharp peaks, excellent resolution, and robust performance—even for challenging sequences and modifications.</p><p>For laboratories developing or refining oligonucleotide workflows, AEX offers both analytical depth and operational confidence.</p><blockquote><p>If you would like to discuss AEX method development or optimization for oligonucleotides, feel free to contact us at <strong>sales@knauer.net</strong>. More insights into practical oligonucleotide analysis will follow in our <i>“Oligos Made Easy”</i> series.</p><p>For technical questions or in-depth discussion, the author can be reached at <strong>kindler@knauer.net</strong></p></blockquote>

Oligos Made Easy - Part 2: AEX

News from LabRulezLCMS Library - Week 07, 2026

Article

Application

Plastics

Environment

Science and research

Poster

RECETOX (Research Centre for Toxic Compounds in the Environment) is an independent department of the Faculty of Science of Masaryk University in Brno, which has been established in 1983. RECETOX is focused on the research and education in cross-cutting area of Environment and Health. It addresses interactions among chemicals, environment, and biological systems, including consequences at local, regional, and global levels.

RECETOX - Centrum pro výzkum toxických látek v prostředí

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<div container-id="cq-colctrl-lt8" comp-id="B1"><div><h3><strong>Acquire high-quality data, regardless of your mass spectrometry platform</strong></h3></div></div><div container-id="cq-colctrl-lt8" comp-id="B2"><div><p><strong>Confidently control, acquire, and interrogate data from a range of Thermo Scientific LC-MS systems and related instruments using Thermo Scientific Xcalibur software.</strong></p><p>With simple method set-up, data acquisition, in-depth data interrogation and reporting tools as well as seamless integration to a range of additional Thermo Scientific application-specific software and cloud-based tools, Xcalibur software serves as the powerful, yet easy-to-use platform for your LC-MS analyses.</p><div><h3><strong>Key benefits of Xcalibur data acquisition software</strong></h3><h5><strong>Comprehensive toolset and landing page for all your installed applications</strong></h5><p>With a homepage that conveniently hosts all your installed applications and provides easy access to instrument control, method development, data acquisition, and reviewing, Xcalibur software makes it quick and easy to navigate through your workflows.</p><h5><strong>Ad-hoc data reviewing and quantitative capabilities</strong></h5><p>When you need to interrogate your data—from elemental compositions, plotting chromatograms, spectral views, performing library searches and much more—or perform basic quantitation, the <strong>FreeStyle and Quan Browser applications included with the Xcalibur software</strong> allow you to gain insights into your data.</p><h5><strong>Integration with cloud-based tools for productivity</strong></h5><p>The landing page for the Xcalibur software not only serves as the configurable portal to your applications, you can also receive application update information, ensuring that you have the latest version of software. Additionally, cloud-based applications allow you to remotely monitor your systems and drive productivity.</p><h3><strong>About Xcalibur data acquisition software</strong></h3><div><p>The <strong>customizable landing page (or Roadmap View) </strong>enables easy access to all your installed applications, from those included with Xcalibur software to your application-specific software packages.</p><p>Not only can you receive notification when there is a new version of any installed application, you can also access the <a target="_blank" rel="noopener noreferrer" href="https://thermo.flexnetoperations.com/control/thmo/login" aria-label="XApp Store - open in a new tab" data-uw-rm-ext-link="" uw-rm-external-link-id="https://thermo.flexnetoperations.com/control/thmo/login$xappstore"><strong>XApp Store</strong></a> for more information on the latest applications and try many of them for free for 60 days.</p><p>A host of<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong> cloud-based applications </strong></a>are available from the Roadmap View, including <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/lc-ms-data-acquisition-software/xcalibur-data-acquisition-interpretation-software.html?open=almanac#almanac"><strong>Almanac</strong></a>, which allows for web- or smartphone-based monitoring of your MS.</p><figure class="image"><img style="aspect-ratio:740/400;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_35361ffe4b.jpg" alt="Thermo Scientific™ Xcalibur™ Software: The customizable landing page (or Roadmap View)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_35361ffe4b.jpg 245w," sizes="100vw" width="740" height="400"></figure><div><p>Regardless of the experimental design, it should be easy to set-up your mass spectrometer to acquire high-quality data. <strong>The Method Editor allows you to quickly and simply create acquisition methods</strong> that control the necessary parameters and drive your acquisition requirements.</p><p>For the <strong>latest generation of mass spectrometers,</strong> there are numerous <strong>pre-configured method templates </strong>arranged by application area. These methods allow users of any experience level to acquire data relevant to their questions. Alternatively, the templates can be used as a starting point to facilitate rapid method development. Each method covers all instrument parameters as well as those for data acquisition, reducing complexity of set up.</p><figure class="image"><img style="aspect-ratio:740/410;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_2_baa5610a5d.jpg" alt="Thermo Scientific™ Xcalibur™ Software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_2_baa5610a5d.jpg 245w," sizes="100vw" width="740" height="410"></figure><div><p>Modern visualization tools allow you to rapidly answer questions as you qualitatively interrogate your data.</p><p>The <strong>FreeStyle application,</strong> <strong>provided with the Xcalibur software</strong>, allows you to interact with your data from simple chromatographic detection and integration to spectral library searching, spectral deconvolution or diagnostic plots.</p><figure class="image"><img style="aspect-ratio:740/400;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_3_221d41f756.jpg" alt="Thermo Scientific™ Xcalibur™ Software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_3_221d41f756.jpg 245w," sizes="100vw" width="740" height="400"></figure><div><p><strong>For rapid quantitation of a small number of targets, </strong><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/lc-ms-data-acquisition-software/xcalibur-data-acquisition-interpretation-software.html?open=quan#quan"><strong>Quan Browser</strong></a><strong>, included with the Xcalibur software, </strong>allows you to quickly identify component peaks, determine integration criteria, and visualize calibration curves, integrations, and results.</p><p><strong>Xcalibur software allows you to interactively edit </strong>processing parameters, report data and rapidly access your quantitative information while processing your quantitation sequences.</p><figure class="image"><img style="aspect-ratio:740/410;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_4_40201472f4.jpg" alt="Thermo Scientific™ Xcalibur™ Software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_4_40201472f4.jpg 245w," sizes="100vw" width="740" height="410"></figure><h3><strong>FreeStyle data review application for Xcalibur software</strong></h3><div colctrl-id="2-1"><div><div container-id="cq-colctrl-lt8" comp-id="B1"><div><p><strong>For the qualitative analysis of any mass spectral data (.raw or .sld) in a highly visual environment, FreeStyle allows you to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, and view the status of various instrument parameters during data acquisition.</strong></p></div></div></div></div><figure class="image"><img style="aspect-ratio:800/195;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_5_6a0f093b2f.jpg" alt="Thermo Scientific™ Xcalibur™ Software: FreeStyle data review application for Xcalibur software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_5_6a0f093b2f.jpg 245w," sizes="100vw" width="800" height="195"></figure><div><p>With a familiar interface, the tools needed to access the information stored in your data are readily accessible. <strong>HRAM</strong> data intelligence means that <strong>data is displayed according to the mass accuracy of the MS system used to acquire it.</strong></p><p><strong>When it comes to visualizing your data, </strong>make use of unlimited plots, quick creation of plots from spectra, spectral annotation with structures, text and graphics, trending/diagnostic plots for status parameters, and scan header entries; float/dock/hide multiple windows and split across monitors to really get the most out of your data.</p><figure class="image"><img style="aspect-ratio:740/400;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_6_e6a704b2dc.jpg" alt="Thermo Scientific™ Xcalibur™ Software: FreeStyle data review application for Xcalibur software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_6_e6a704b2dc.jpg 245w," sizes="100vw" width="740" height="400"></figure><p><strong>Create and customize highly visual map views of complex datasets</strong>, with simple modification of any plots and data views. Then use those views to generate your own visual reports, enhancing your insights.</p><figure class="image"><img style="aspect-ratio:740/420;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_7_1ac807c5fa.jpg" alt="Thermo Scientific™ Xcalibur™ Software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_7_1ac807c5fa.jpg 245w," sizes="100vw" width="740" height="420"></figure><p><strong>High-resolution protein mass spectral data </strong>can be deconvoluted using <strong>the Xtract deconvolution algorithm</strong>, contained in the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1837"><strong>Thermo Scientific BioPharma Finder</strong></a><strong> software</strong> to obtain the intact mass and a single, deconvoluted mass spectrum for the protein components within the charge state envelope.</p><figure class="image"><img style="aspect-ratio:740/420;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_8_c6820a5e8c.jpg" alt="Thermo Scientific™ Xcalibur™ Software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_8_c6820a5e8c.jpg 245w," sizes="100vw" width="740" height="420"></figure><div><p>Discovering what is in your data doesn’t need to be challenging. The ability to search the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud</strong></a><strong> mass spectral library,</strong> <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1760"><strong>mzVault</strong></a>,<strong> or NIST </strong>with a single-click means that compound identification from MS and MS<sup>2</sup> data is quick and easy. You can also export spectral data to the NIST application.</p><p>Elemental compositions can be calculated using MS and MS<sup>2</sup> data, with isotopic simulations for added confidence.</p></div><div><h3><strong>Quan Browser application for Xcalibur software</strong></h3><div><div container-id="cq-colctrl-lt8" comp-id="B1"><div><p><strong>When you require a quick answer, the Quan Browser, included in the Xcalibur software, allows you to determine the concentration of analytes within your sample set when there is a small number of targets.</strong></p><figure class="image"><img style="aspect-ratio:800/195;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_9_781c806926.jpg" alt="Thermo Scientific™ Xcalibur™ Software: Quan Browser application for Xcalibur software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_9_781c806926.jpg 245w," sizes="100vw" width="800" height="195"></figure><p>You can <strong>review or rework </strong>your component peak identifications and integration criteria, calibration curves for your quantitation standards, your standards, QC samples, blanks and unknowns with interactive editing of processing parameters.</p><figure class="image"><img style="aspect-ratio:740/385;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Xcalibur_Software_10_55b04eedae.jpg" alt="Thermo Scientific™ Xcalibur™ Software: Quan Browser application for Xcalibur software." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Xcalibur_Software_10_55b04eedae.jpg 245w," sizes="100vw" width="740" height="385"></figure><p><strong>The Quan Browser, included in the Xcalibur software,</strong> incorporates a results view where you can observe the data used to create calibration curves and peak integrations. Quantitation sequences, including bracketed sequences, can be processed, and any processing parameters interactively edited with the results are dynamically updated.</p><p>For <strong>larger quantitative studies</strong> we recommend either<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/77"><strong>Thermo Scientific TraceFinder software</strong></a><strong> </strong>for high-throughput analyses, or <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong>Thermo Scientific Chromeleon Chromatography Data System (CDS) software</strong></a> for regulated studies, such as regulated bioanalysis, which require tools for compliance.</p></div></div></div></div></div></div></div></div></div></div></div></div>

Thermo Scientific Compound Discoverer software

Compound Discoverer software addresses small molecule identification needs and workflows including untargeted metabolomics, drug metabolism, impurity, E&L, environmental, food & beverage, and forensic research.

Thermo Scientific mzVault offline advanced mass spectral database

mzVault provides you the capabilities to access and search mzCloud’s MS2-level spectral data off-line, or to store your own spectral library information.

<p><strong>Your data has inherent value, as it is the knowledge that you acquire. mzVault provides you the capabilities to access and search mzCloud’s MS<sup>2</sup>-level spectral data off-line, or to store your own spectral library information. Spectral information, and your knowledge, can be automatically sent from </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer</strong></a><strong> into a new, or existing library which can then be searched using Compound Discoverer or</strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong> Mass Frontier.</strong></a></p><div><p>When you need to curate proprietary libraries and ensure the highest quality data, <strong>Mass Frontier</strong> provides you with the same tools used to curate <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud</strong></a>, meaning that <strong>you can ensure your spectral data has been filtered, recalibrated, averaged and fully structurally annotated, ready to share your knowledge within your organization.</strong></p></div><div><h3><strong>Key benefits</strong></h3><h5><strong>Know more unknowns off-line</strong></h5><p><strong>Sometimes it isn’t possible to be online and access </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud</strong></a><strong>.</strong> mzVault contains all MS<sup>2</sup>-level spectral data contained within mzCloud to allow for confident unknown identifications.</p><h5><strong>Create and share your knowledge&nbsp;&nbsp;&nbsp;&nbsp;</strong></h5><p><strong>Create, store and search your own in-house spectral libraries. </strong>Once you have identified unknowns through mzLogic, or you have your proprietary compounds, make sure that this valuable information can be leveraged.</p><h5><strong>Have I seen this unknown before?&nbsp;&nbsp;&nbsp;&nbsp;</strong></h5><p><strong>Even with extensive online structural databases, and mzLogic to propose a structure or sub-structure, there can be occasions where it remains an unknown.</strong> Store this information and re-use to see if you have previously observed any unknowns.</p><h5><strong>Curate your high-quality data</strong></h5><p><strong>When it is important to curate your valuable data</strong>, the <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.html?open=curator">Curator</a> tool from Mass Frontier allows you to use the same tools used to populate <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud</strong></a>, ensuring the creation of your own high-quality mzVault proprietary libraries.</p></div>

Thermo Scientific Metabolika module for easy pathway analysis

Create, edit and search reaction pathways using the new Metabolika module to take your knowledge to the next level. 

<div style="height:auto;" id="metabolika"><div><div><div><div colctrl-id="7-1"><div><div container-id="cq-colctrl-lt8" comp-id="B1"><div><p><strong>Create, edit and search reaction pathways using the new Metabolika module to take your knowledge to the next level. With publication-quality graphical functionality to create and edit reaction pathways within</strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong> Thermo Scientific Compound Discoverer 3.0</strong></a><strong> or greater, and </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong>Thermo Scientific Mass Frontier Software 8.0</strong></a><strong> or greater, and more than 370 curated and annotated biochemical pathways for a range of organisms, it is easier than ever to share your pathway knowledge.</strong></p><p>The Metabolika Module is also utilized within substructure searching, fragmentation prediction and for <strong>mzLogic</strong>, further increasing the chances of unknown compound identification.</p></div></div></div></div><div><p>When used within the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer software</strong></a>, this module can take your data visualization to a new level with interactive statistical data overlay, including metabolic flux analysis data.</p><div><h3><strong>Key benefits</strong></h3><h5><strong>Create, edit and store reaction pathways&nbsp;&nbsp;&nbsp;&nbsp;</strong></h5><p>From the included &gt;370 metabolic pathways, through to your own reaction pathways, easily curate and edit your knowledge for future use within both the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer</strong></a> and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong>Mass Frontier</strong></a> software.</p><h5><strong>Access knowledge of &gt;370 metabolic pathways&nbsp;&nbsp;&nbsp;&nbsp;</strong></h5><p>The combined knowledge of the included pathways isn’t just restricted to Metabolika, the information is also fully utilized for substructure searching as well as with<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1762"> <strong>mzLogic</strong></a><strong>.</strong></p><h5><strong>Map pathways to your data, as well as visualize your statistical information</strong></h5><p>Pathways can be easily mapped to your detected compounds within the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer software</strong></a>, with highly visual and interactive representation. Additionally, your statistical information from flux analyses can be displayed within Metabolika pathways for easy data visualization.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Metabolika_module_for_easy_pathway_analysis_781f11c926.jpg" alt="Thermo Scientific Metabolika module for easy pathway analysis: An example of Metabolika pathways analysis tool with flux analysis data included, showing qualitative flux analysis of exchange rates from a stable isotope labeling experiment." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Metabolika_module_for_easy_pathway_analysis_781f11c926.jpg 245w," sizes="100vw" width="960" height="500"></p></div></div></div></div></div></div>

Thermo Scientific mzLogic Data Analysis Algorithm

mzLogic solves a key challenge in small molecule identification by enabling the characterization of unknowns when high-quality MSⁿ data yield no matches in spectral libraries.

<div style="height:auto;" id="mzlogic"><div><div style="display:block;"><div><div><div container-id="cq-colctrl-lt8" comp-id="B2"><div><div><div container-id="cq-colctrl-lt8" comp-id="B1"><div><h3><strong>Accelerate unknown small molecule identification with mzLogic</strong></h3></div></div><div container-id="cq-colctrl-lt8" comp-id="B2"><div><p><strong>The mzLogic data analysis algorithm addresses one of the biggest challenges for small molecule characterization and identification-when, despite having sufficient high-quality and high-resolution MS<sup>n</sup> mass spectrometric data, there is no match in any spectral library, meaning you have an unknown.</strong></p><p>mzLogic combines the extensive fragmentation information available within the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud</strong></a> online advanced mass spectral library with the information in numerous online structural databases. As a result, mzLogic allows you to take thousands of potential structural candidates and automatically rank them based upon spectral similarity and sub-structural information – delivering confident candidates for your true unknowns.</p></div></div></div></div></div></div><div><h3><strong>Key benefits</strong></h3><h5><strong>Combine the benefits of multiple libraries and databases&nbsp;&nbsp;&nbsp;&nbsp;</strong></h5><p>The ability of mzLogic to combine the extensive, high-quality and high-resolution accurate mass, multi-stage (MS<sup>n</sup>) fragmentation information in <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764">mzCloud</a>, with numerous online structural databases provides the greatest chance to confidently identify unknowns.</p><h5><strong>Take lengthy guesswork out of unknown identification&nbsp;&nbsp;&nbsp;&nbsp;</strong></h5><p>mzLogic uses the data from <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764">mzCloud </a>and multiple other data sources to identify common sub-structural features from your MS<sup>n</sup> data, explaining as much of your fragmentation data as possible before the next stages of identification.</p><h5><strong>Go from thousands of potential candidates to a handful</strong></h5><p>Using elemental composition to search structural databases can return thousands of potential candidates; mzLogic uses MS<sup>n</sup> data and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764">mzCloud</a> fragmentation database information to explain as much structural information as possible, reducing thousands of potentials to a handful of confident candidates based upon structural similarity.</p><div><div><figure class="image"><img style="aspect-ratio:740/345;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_05478bcf43.jpg" alt="Thermo Scientific mzLogic Data Analysis Algorithm: Take the guesswork out of small molecule unknown identification through the combination of mzLogic algorithm and the high quality, structurally diverse mass spectral fragmentation information contained within mzCloud, to propose and confirm structural identification." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_05478bcf43.jpg 245w," sizes="100vw" width="740" height="345"></figure><h3><strong>How does your data relate to mass spectral libraries?</strong></h3><div style="height:auto;" id="massspectrallibraries"><div><div><div><div><p>Whether you are working to better characterize and understand <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/cz/en/home/industrial/pharma-biopharma/pre-clinical-and-clinical-drug-testing/metabolite-identification.html">metabolism and drug analytes</a>, <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/cz/en/home/industrial/food-beverage/food-analytical-testing/food-contact-materials.html">food and environmental samples</a>, <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/cz/en/home/industrial/forensics/antidoping/doping-control-retrospective-analysis.html">designer drugs</a> or <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/cz/en/home/industrial/pharma-biopharma/pharma-biopharma-learning-center/pharmaceutical-qa-qc-information/extractables-leachables-information.html">extractables and leachables</a>, the use of mass spectral libraries and online databases can help identify compounds in your samples. However, with increasing crossover between compound classes, new impurities, subtle compound transformations or metabolism and degradation products, sometimes no compelling match is made to the libraries you use.</p><p>Acquiring comprehensive high-resolution accurate- mass MS/MS and MS<sup>n</sup> data has been simplified with data acquisition tools such as <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1763"><strong>AcquireX</strong></a>, and general hardware improvements. Obtaining mass spectral libraries that contain broad chemical diversity, extensive fragmentation and reliable and concise data has been the biggest challenge.</p><p>The<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764">mzCloud</a> mass spectral database is the largest (in terms of total spectra and data per compound) publicly available online mass spectral fragmentation library. It contains high-resolution accurate-mass (HRAM) spectra, including exhaustive high-resolution MS/MS and multi-stage MS<sup>n</sup> spectra. Each entry contains considerable metadata and, most importantly, has been extensively curated (i.e., filtered, recalibrated, averaged, and annotated) to provide absolute confidence in the quality of its contents.</p><figure class="image"><img style="aspect-ratio:908/323;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_2_959e175e53.jpg" alt="Thermo Scientific mzLogic Data Analysis Algorithm: High quality MS, MS/MS and MSn data can be used to interrogate the fully curated and annotated mass-spectral fragmentation library, mzCloud. Common substructural information can be used from the extensive fragmentation information to aid in unknown compound identification using mzLogic algorithm." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_2_959e175e53.jpg 245w," sizes="100vw" width="908" height="323"></figure><h3><strong>How does mzLogic identify unknowns?</strong></h3><div style="height:auto;" id="identifyunknowns"><div><div><div><div><p>Each <strong>mzCloud library</strong> entry contains extensive fragmentation information, which has been acquired using both a range of collision energies and fragmentation techniques (collision induced and higher energy collisional dissociation, CID and HCD). When this information is combined with the broad chemical diversity of library entries, the likelihood that some or all of an unknown structure can be matched against an existing fragment within the library increases.</p><figure class="image"><img style="aspect-ratio:927/394;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_3_b50ae0af70.jpg" alt="Thermo Scientific mzLogic Data Analysis Algorithm: mzLogic reduction of putative candidates using online structural databases and the extensive fragmentation information contained within mzCloud." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_3_b50ae0af70.jpg 245w," sizes="100vw" width="927" height="394"></figure></div></div></div></div></div><div style="height:auto;" id="identifyunknowns"><div><div><div><div><p>As shown in the figure above, mzLogic is available as part of the<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong> Mass Frontier software</strong></a> and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer software</strong></a> packages, and works as follows:</p><ol style="list-style-type:upper-latin;"><li>Online databases, such as <a target="_blank" rel="noopener noreferrer" href="http://www.chemspider.com" aria-label="ChemSpider - open in a new tab" data-uw-rm-ext-link="" uw-rm-external-link-id="http://www.chemspider.com/$chemspider">ChemSpider</a>, which contains more than 70 million structures, can be searched using an elemental composition. Even with the ability to use the high-resolution and accurate mass capabilities of <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;search=orbitrap"><strong>Orbitrap mass analyzers</strong></a> to reveal fine isotopic information, many hundreds or even thousands of potential structures could match the elemental composition.</li><li>The high-quality fragmentation information contained within mzCloud is <strong>compared to experimental data.</strong></li><li>mzLogic rapidly identifies structurally similar fragments through forward and reverse searches.</li><li>Based upon the identified sub-structures, the structural candidates from the online search are ranked in order of how much of the structure can be explained through the sub-structural matching.</li><li>This ranking based upon the use of real data, takes many hundreds or thousands of potential candidates and reduces them to a significantly smaller list of putative structures, with visualization tools to explain the ranking and structure accounted for by library fragments.</li></ol><div><div><h3><strong>What is the next step to confirm any potential candidates?</strong></h3><div style="height:auto;" id="potentialcandidates"><div><div><div><div><p>The ranked results from using mzLogic will either show that all the structure can be accounted for in that candidate or that there is still some structural information from the proposed candidate that cannot be accounted for. MS/MS and/or MS<sup>n</sup> fragmentation spectra typically contains substantial amounts of structural information, which can be further investigated using <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer</strong></a> or <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong>Mass Frontier software</strong></a>.</p><p>Where a complete, in-depth analysis of MS<sup>n</sup> fragmentation data is required,<strong> </strong>Mass Frontier software provides visualization and understanding of fragmentation pathways using extensive MS<sup>n</sup> data. The<strong> Fragments and Mechanism tool </strong>simulates unimolecular dissociation of the proposed structures, including rearrangements and predicted fragments, and can be used to explain the experimental fragmentation data through fragment annotations to help identify which candidates are indeed plausible. Rather than coded fragmentation algorithms, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1757"><strong>Mass Frontier software</strong></a><strong> bases fragmentation on mechanisms published in more than 95% of all peer-reviewed scientific journals.</strong></p><p>This approach adds greater certainty to putative structure identification through the deep fragmentation and characterization information provided by the high-quality data and extensive spectral trees in <strong>mzCloud.</strong></p><figure class="image"><img style="aspect-ratio:673/324;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_4_1d09064e9e.jpg" alt="Thermo Scientific mzLogic Data Analysis Algorithm: Confident structural elucidation using automated fragmentation annotation of MSn spectral trees. Fragmentation pathways can also be predicted based upon submission of a structure and makes full use of the HighChem Fragmentation Library. This library contains information from more than 52,000 fragmentation schemes, 217,000 individual reactions, 256,000 chemical structures and 216,000 decoded mechanisms from peer reviewed literature." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Logic_Data_Analysis_Algorithm_4_1d09064e9e.jpg 245w," sizes="100vw" width="673" height="324"></figure></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>

Thermo Scientific AcquireX Intelligent Data Acquisition Workflow

The Thermo Scientific AcquireX workflow enhances LC-MSn data acquisition by automating and connecting experiments for efficient, intelligent small-molecule analysis across five different routines.

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>

Thermo Scientific Proteome Discoverer Software

Identify and quantify peptides and proteins in complex biological samples using Thermo Scientific™ Proteome Discoverer™ software. 

<h3><strong>Comprehensive, extensible, and intelligent platform</strong></h3><p><strong>Thermo Scientific Proteome Discoverer Software is the ultimate toolbox for protein research, offering customizable workflows tailored to the complexities of modern proteomics. It simplifies the identification and quantification of proteins in complex biological samples, supporting a wide range of workflows, including peptide and protein identification, post-translational modifications (PTM) analysis, isobaric mass tagging, and label-free quantitation (LFQ). It handles data from diverse acquisition methods, such as data-independent acquisition (DIA), data-dependent acquisition (DDA), and wide window acquisition (WWA), ensuring comprehensive coverage.</strong></p><p><strong>Advanced tools </strong>like INFERYS™ Rescoring and the CHIMERYS™ intelligent search algorithm by MSAID significantly increase identification rates, protein coverage, and the discovery of unique peptides and PTMs. The software enhances protein quantitation for isobaric mass tags and LFQ, supporting multiple database search algorithms and dissociation techniques. Whether analyzing glycopeptides, top-down proteomics, proteoforms, or MS-based structural biology like chemical cross-linking (XL-MS), Proteome Discoverer Software enables scientists to extract deeper biological insights from their data.</p><figure class="image"><img style="aspect-ratio:1131/598;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Proteome_Discoverer_Software_7_2221d76acd.jpg" alt="Thermo Scientific Proteome Discoverer Software: Proteome Discoverer software in peer reviewed articles." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Proteome_Discoverer_Software_7_2221d76acd.jpg 245w," sizes="100vw" width="1131" height="598"></figure><h3><strong>Key benefits</strong></h3><h5><strong>Customize your data analysis</strong></h5><p>Use the node-based workflow editor to customize your data analysis for maximum coverage and confidence. Integrate database search results from multiple search engines such as SEQUEST™ HT, Mascot, MSAmanda, Byonic™ from Protein Metrics, and<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1756"><strong>Thermo Scientific ProSightPD</strong></a> software. Increase confidence in peptide identification and quantification using INFERYS Rescoring and enable a deeper mining of your DIA, DDA, or WWA data using the CHIMERYS intelligent search algorithm.</p><h5><strong>Perform relative quantitation</strong></h5><p>Measure and report the relative expression levels of isotopically labeled peptides for:</p><ul><li>TMT SPS MS3</li><li>Glycopeptide identification and quantification</li><li>Phosphopeptide identification and quantification</li><li>Top-down proteomics</li><li>Cross-linking</li></ul><p>Confidently and efficiently interpret your data with integrated statistical and visualization tools for a faster time to meaningful results.</p><h5><strong>Extensible workflow tools</strong></h5><p>Utilize third-party nodes and build in customization with the scripting node, while maintaining full integration into the Proteome Discoverer software framework to leverage visualization, statistical analysis, and biological interpretation tools to take your analysis to the next level.</p><figure class="image"><img style="aspect-ratio:1160/533;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Proteome_Discoverer_Software_4_4d8ae8fcd2.jpg" alt="Thermo Scientific Proteome Discoverer Software: Extensibility - Connect to external tools via the Scripting Node; Integration with MSstatsTMT via custom script." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Proteome_Discoverer_Software_4_4d8ae8fcd2.jpg 245w," sizes="100vw" width="1160" height="533"></figure><h3><strong>Comprehensive tools for proteomic studies</strong></h3><p>With a wide range of database search options and the ability to combine the output from multiple algorithms, Proteome Discoverer software increases confidence in results and decision making through cross-validation. Augment searches with intelligent<strong> INFERYS Rescoring</strong> to increase confidence in peptide identification and quantitation. Whether you acquire your data in <strong>DIA, DDA, or WWA mode, CHIMERYS</strong> <strong>intelligent search algorithm </strong>helps you dig deeper into your data to substantially increase the number of unique peptide identifications, improve protein coverage, extend quantitation capabilities, and uncover new insights.</p><p>Complete sequence coverage and confident identification of post-translational modifications (PTMs) is realized with support for multiple dissociation techniques including collision-induced dissociation (CID), higher-energy collision-induced dissociation (HCD) and electron-transfer dissociation (ETD) in tandem with built-for-purpose search engines.</p><h3><strong>Customizable data analysis workflows</strong></h3><p><strong>Automate and simplify data analysis</strong> through customizable workflows including full support for multiple quantitative workflows. Enjoy experimental flexibility for quantitation by employing isobaric mass tagging with TMT and TMTpro reagent or other isotopic labeling strategies or utilize label-free quantitation techniques. Map quantitative data to biological information through study management and leverage fast, robust algorithms for peak selection and peptide quantification to extract the maximum possible information from quantitative proteomics studies.</p><p>Refine acquisition strategies by generating inclusion and exclusion lists that can be directly imported into instrument methods. Confidently and easily facilitate data comparison, exchange, and verification in compliance with data standards developed by the HUPO Proteomics Standards Initiative (PSI).</p><figure class="image"><img style="aspect-ratio:1232/459;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Proteomics_Software_Solution_98e62449c5.jpg" alt="Thermo Scientific Proteome Discoverer Software: The workflow system in Proteome Discoverer allows for customizable workflows to analyze complex proteomics data. The workflow system is composed of nodes that can connect in linear or branched pathways. While these workflows are highly customizable, pre-defined workflows for common workflows such as TMT, LFQ, PTM identification and cross-linked peptide ID are included." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Proteomics_Software_Solution_98e62449c5.jpg 245w," sizes="100vw" width="1232" height="459"></figure><h5><strong>Interactive enrichment table from graphical results to find overrepresented pathways</strong></h5><figure class="image"><img style="aspect-ratio:1344/924;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Proteome_Discoverer_Software_3_c01db3165a.jpg" alt="Thermo Scientific Proteome Discoverer Software: Interactive enrichment tables allow for the selection of up- or down-regulated proteins or peptides in any view, including volcano plots, PCA plots, and heat maps, and the visualization of corresponding Reactome pathways from the checked proteins to help derive biological interpretation of results. In addition to Reactome pathways, KEGG and Wikipathways as well as gene ontology terms and protein families can be visualized in the enrichment table." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Proteome_Discoverer_Software_3_c01db3165a.jpg 227w," sizes="100vw" width="1344" height="924"></figure><h5><strong>Pathway maps</strong></h5><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Proteome_Discoverer_Software_5_c087bb9d6f.jpg" alt="Thermo Scientific Proteome Discoverer Software: Pathways can also be directly visualized, providing biological context and background literature references using pathway maps." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Proteome_Discoverer_Software_5_c087bb9d6f.jpg 245w," sizes="100vw" width="1119" height="584"></p><h5><strong>Interactive data visualization</strong></h5><figure class="image"><img style="aspect-ratio:973/879;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Proteome_Discoverer_Software_6_2b32110442.jpg" alt="Thermo Scientific Proteome Discoverer Software: Interactive data visualization." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Proteome_Discoverer_Software_6_2b32110442.jpg 173w," sizes="100vw" width="973" height="879"></figure>

Thermo Scientific™ SimGlycan™ Software

SimGlycan software processes and interprets the multi-stage/sequential (MSn) data produced by Thermo Scientific™ Mass Spectrometers, a capability essential to determining glycan heterogeneity and isomeric forms.

<p><strong>Speed the characterization of complex glycans using SimGlycan™ software from PREMIER Biosoft. SimGlycan software processes and interprets the multi-stage/sequential (MS<sup>n</sup>) data produced by Thermo Scientific™ Mass Spectrometers, a capability essential to determining glycan heterogeneity and isomeric forms.</strong></p><p>The software automatically matches experimental mass spectra against a comprehensive database and generates a scored list of candidate structures.</p><h3><strong>Comprehensive Analyses</strong></h3><ul><li>Supports all Thermo Scientific ion trap and Orbitrap™-based instruments performing glycan characterization</li><li>Processes MS<sup>n</sup> data to resolve glycan heterogeneity, branching patterns, and isobaric structures. Up to seven levels of MS fragmentation can be needed to differentiate between glycan structural isomers</li><li>Includes a database of over 22500 glycans to process and verify structures</li><li>Provides a wealth of relevant biological information for the probable glycan structure, including glycan class, reaction, pathway, and enzyme</li><li>Searches for glycans with various chemical derivatives used for reducing end modifications, even if the derivative is not available in the database</li><li>Characterizes Na, Li, Mg, K, and formate adducts, and adduct combinations such as Na + H, Li + H, etc.</li><li>Identifies complex glycosaminoglycan structures, even when modified with substituents such as sulfate, phosphate, and ethanolamine</li><li>Determines cross-ring and double glycosidic cleavages, through a combination of permethyl derivatization and MS<sup>n</sup> data</li></ul><h3><strong>Powerful Reporting</strong></h3><ul><li>Creates reports that include glycan characteristics such as ID, sequence, name, composition, mass, precursor ion <i>m/z</i>, class, reaction, pathway, glycan image and theoretical fragments with corresponding mass and <i>m/z</i> values</li><li>Exports images of glycan structures, fragments, and spectra as JPEG or PNG files</li></ul>

Thermo Scientific LC-MS Data Processing Software

 Thermo Scientific LC-MS software streamlines data analysis with application-specific tools for -omics, pharma, and quant. Gain reliable insights to support decisions.

Products from category Software and libraries distributed by Thermo Fisher Scientific (EMEA) - page 2

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