<p><strong>🎤Dr. Christopher Reid (Professor of Chemistry and Biochemistry at Bryant University in Rhode Island)</strong></p><p><strong>In this episode of Concentrating on Chromatography, host Dave Oliva sits down with Chris Reid to explore how chemical biology and LC-MS are being used to tackle one of the most urgent global challenges: antimicrobial resistance.</strong></p><p>As antibiotic resistance continues to rise—and new drug development struggles to keep pace—researchers are looking beyond traditional approaches. Instead of targeting how bacteria build their cell walls, Chris’s work focuses on how they break them down, opening the door to entirely new antimicrobial strategies.</p><h4><strong>What You’ll Learn in This Episode:</strong></h4><ul><li>Why antimicrobial resistance is accelerating globally</li><li>What peptidoglycan is and why it’s essential to bacterial survival</li><li>How targeting cell wall degradation differs from traditional antibiotics</li><li>The strategy behind designing small molecule probes and inhibitors</li><li>How LC-MS is used to analyze peptidoglycan fragments and enzyme activity</li><li>Key analytical challenges: complex mixtures, low-abundance species, and structural similarity</li><li>The importance of sample preparation and reproducibility in LC-MS workflows</li><li>How this research could lead to new antibiotic targets</li></ul><h3><strong>Video Transcription</strong></h3><h4><strong>The Growing Challenge of Antibiotic Resistance</strong></h4><p>According to Reid, antibiotic resistance is increasing across a broad spectrum of bacterial pathogens that were once readily treated with existing therapies. In some cases, clinicians must now rely on only a handful of last-line antibiotics, while resistance is also rising in diseases such as tuberculosis.</p><p>One of the major obstacles is the limited commercial incentive to develop entirely new antibiotics. Because bacterial resistance can emerge relatively quickly after a drug reaches the market, pharmaceutical companies often favor modifying existing antibiotics or combining them with resistance-modifying agents rather than investing in completely new drug classes. As a result, genuinely novel antibacterial targets remain urgently needed.</p><h4><strong>Why the Bacterial Cell Wall Remains an Attractive Target</strong></h4><p>The bacterial cell wall consists primarily of <strong>peptidoglycan</strong>, a highly cross-linked polymer that provides structural integrity, maintains cell shape, and enables bacterial growth and division.</p><p>Many widely used antibiotics—including the β-lactam antibiotics such as penicillins—target enzymes responsible for synthesizing or cross-linking peptidoglycan. These pathways have proven highly successful therapeutic targets because peptidoglycan is unique to bacteria and absent from human cells, minimizing unwanted effects on the host.</p><p>However, most existing antibiotics target only specific stages of peptidoglycan biosynthesis. Reid's research explores another part of this complex pathway: enzymes responsible for degrading the carbohydrate backbone of peptidoglycan during normal bacterial growth and remodeling. These enzymes may represent an underexplored class of antimicrobial targets capable of overcoming existing resistance mechanisms.</p><h4><strong>Targeting the Glycan Backbone</strong></h4><p>A key advantage of focusing on the carbohydrate backbone is its remarkable conservation across both Gram-positive and Gram-negative bacteria.</p><p>Whereas the peptide components of peptidoglycan vary considerably between bacterial species—and frequently acquire mutations associated with antibiotic resistance—the glycan backbone remains highly conserved and tolerates relatively few structural modifications.</p><p>This biological constraint makes enzymes acting on the glycan backbone particularly attractive targets. Reid's group developed a series of <strong>small-molecule probes and inhibitors</strong> designed to recognize enzymes known as <strong>N-acetylglucosaminidases</strong>, which cleave glycosidic bonds within peptidoglycan and generate soluble degradation products.</p><p>Rather than beginning with purified enzymes, the researchers adopted a <strong>top-down phenotypic screening strategy</strong>. Candidate compounds were first evaluated for their ability to inhibit bacterial growth before progressively narrowing the list of potential molecular targets through genetic studies, microscopy, enzyme assays, and biochemical characterization. This iterative workflow ultimately identified compounds capable of inhibiting the desired enzyme class while simultaneously providing valuable chemical probes for studying bacterial cell wall biology.</p><h4><strong>LC-MS as a Central Analytical Tool</strong></h4><p>Liquid chromatography coupled with mass spectrometry plays a central role throughout the project by enabling detailed characterization of structural changes occurring within peptidoglycan after bacterial cells are treated with candidate inhibitors.</p><p>Because intact peptidoglycan is an insoluble polymer, sample preparation begins with isolation of the bacterial cell wall through detergent extraction and differential centrifugation. Additional purification steps remove proteins, nucleic acids, and teichoic acids before enzymatic digestion converts the insoluble material into soluble fragments suitable for chromatographic analysis.</p><p>The resulting digest is analyzed by LC-MS to examine changes in the distribution of peptidoglycan fragments. Chromatographic retention times provide an immediate indication of changes in cross-linking, with larger oligomers such as trimers and tetramers generally eluting later than monomeric fragments. Mass spectrometry then confirms the identity of these fragments by measuring their intact molecular masses, while tandem MS experiments can provide further structural information when required.</p><h4><strong>Sample Preparation Determines Data Quality</strong></h4><p>Reid emphasized that sample preparation represents one of the most critical—and challenging—stages of the entire workflow.</p><p>Because peptidoglycan analysis involves multiple purification, digestion, and reduction steps, even minor procedural differences between samples can introduce analytical artifacts that complicate biological interpretation.</p><p>Maintaining strict consistency throughout sample preparation is therefore essential. Appropriate controls must accompany every experiment, ensuring that observed chromatographic and mass spectrometric differences truly reflect biological responses rather than experimental variability. The complexity of bacterial cell wall composition further increases the analytical challenge, as subtle differences in amino acid substitutions and low-abundance cross-linked species can complicate LC-MS data interpretation.</p><h4><strong>Chemical Biology for Future Antibiotic Discovery</strong></h4><p>Although the identified compounds may eventually serve as starting points for antibiotic development, Reid views them primarily as <strong>chemical biology tools</strong>.</p><p>By selectively inhibiting individual enzymes, these probes allow researchers to investigate previously unexplored aspects of bacterial cell wall remodeling that cannot easily be studied using classical genetic approaches alone.</p><p>The research team is now expanding this strategy by combining their probes with <strong>proximity-labeling proteomics and mass spectrometry</strong>, aiming to map protein interaction networks associated with bacterial cell wall degradation. Such studies may reveal entirely new antibacterial targets and provide deeper insight into the biological processes governing bacterial growth and division.</p><p>Ultimately, the work illustrates how integrating synthetic chemistry, microbiology, molecular biology, and advanced LC-MS can accelerate the search for innovative therapeutic strategies against antimicrobial resistance. As existing antibiotics become progressively less effective, multidisciplinary approaches such as these may play an increasingly important role in identifying the next generation of antibacterial targets.</p><blockquote><p><strong>This text has been automatically transcribed from a video presentation using AI technology. It may contain inaccuracies and is not guaranteed to be 100% correct.</strong></p></blockquote><blockquote><h4><strong>Concentrating on Chromatography Podcast</strong></h4><p>Dive into the frontiers of chromatography, mass spectrometry, and sample preparation with host David Oliva. Each episode features candid conversations with leading researchers, industry innovators, and passionate scientists who are shaping the future of analytical chemistry. From decoding PFAS detection challenges to exploring the latest in AI-assisted liquid chromatography, this show uncovers practical workflows, sustainability breakthroughs, and the real-world impact of separation science. Whether you’re a chromatographer, lab professional, or researcher you'll discover inspiring content!</p><p>You can find <strong>Concentrating on Chromatography Podcast </strong>in podcast apps:</p><ul><li><a target="_blank" rel="noopener noreferrer" href="https://open.spotify.com/show/1wZg67rCjoGju4yhqxI3tL"><strong>Spotify</strong></a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podcasts.apple.com/tz/podcast/concentrating-on-chromatography/id1788429185"><strong>Apple podcast</strong></a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podscan.fm/podcasts/concentrating-on-chromatography"><strong>podscan</strong></a></li></ul><p>and on <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@ChromatographyTalk/videos"><strong>YouTube channel</strong></a></p></blockquote>

 Fighting Antibiotic Resistance with LC-MS: Targeting Bacterial Cell Walls

<p><strong>This study compares a commercial ELISA assay with a validated UHPLC-MS/MS method for determining total ergot alkaloids in wheat and durum samples. In addition to method performance, the authors investigated cross-reactivity and matrix effects to explain differences between immunoassay and chromatographic results.</strong></p><p>While ELISA demonstrated good repeatability and is well suited for high-throughput screening, systematic biases were observed due to compound- and matrix-dependent cross-reactivity. The findings support ELISA as an effective screening tool, whereas UHPLC-MS/MS remains the preferred method for accurate quantification and regulatory confirmation of ergot alkaloids.</p><blockquote><h4><strong>The original article</strong></h4><h4><a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jafc.6c05234"><strong>Comparative Evaluation of Total Ergot Alkaloids Determination by ELISA and UHPLC-MS/MS in Wheat: Implications of Cross-Reactivity and Matrix Effects</strong></a></h4><p>Chamali Kodikara*, Dainna Drul, Nandika Bandara, and Sheryl A. Tittlemier*</p><p>J. Agric. Food Chem. 2026, 74, 25, 20015–20027</p><p><a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1021/acs.jafc.6c05234">https://doi.org/10.1021/acs.jafc.6c05234</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><p><strong>Selected sections from the article follow. Formats and hyperlinks were adapted from the original.</strong></p><div><p>Ergot alkaloids (EAs) are a structurally diverse group of indole-derived mycotoxins produced primarily by phytopathogenic fungi of the genus <i>Claviceps</i>, most notably <i>Claviceps purpurea</i>. These fungi infect the flowering heads of cereal crops, replacing the developing grain with hardened fungal structures (sclerotia) that contain ergot alkaloids. Cereals such as rye, wheat, barley, oats, and triticale are particularly susceptible, with infection severity strongly influenced by environmental conditions during flowering, including rainfall and humidity. <a href="javascript:void(0);">(1−3)</a> Although improvements in agronomic practices and grain cleaning have reduced the prevalence of visible ergot sclerotia, ergot alkaloids can persist in cereals and cereal-based foods even in the absence of detectable sclerotia. This may occur because sclerotia can fragment during harvesting, handling, cleaning, or milling, producing small particles that are not visually detected but may still contribute ergot alkaloids to grain or processed products, continuing to pose food and feed safety concerns. <a href="javascript:void(0);">(4)</a> <a href="javascript:void(0);">(5)</a> Ergot alkaloids share a common tetracyclic ergoline backbone and occur as structurally related compounds, including ergometrine, ergotamine, ergosine, ergocristine, ergocryptine, and ergocornine, together with their corresponding C-8 epimers. These epimers occur as <i>R-</i> and <i>S-</i>configurations, commonly referred to as -ine and -inine forms, respectively. Epimerization at the C-8 position can occur during fungal metabolism and during sample extraction, storage, and analysis, complicating accurate quantification. <a href="javascript:void(0);">(6,7)</a> Although S-epimers were historically considered biologically inactive, recent evidence indicates that they may contribute to overall exposure and toxicity, supporting their inclusion in analytical and regulatory frameworks. <a href="javascript:void(0);">(3)</a></p><p>Dietary exposure to elevated levels of ergot alkaloids has been associated with a range of adverse health effects, collectively referred to as ergotism, including vasoconstriction, ischemia, neurological disturbances, and hallucinations. <a href="javascript:void(0);">(3)</a> These effects arise primarily from interactions with adrenergic, serotonergic, and dopaminergic receptors. <a href="javascript:void(0);">(8−10)</a> In response, regulatory limits for ergot alkaloids in food have been introduced or revised in several jurisdictions. In the European Union, maximum levels have been established for the sum of 12 ergot alkaloids in cereal milling products under Regulation (EU) 2021/1399, which was subsequently consolidated under Regulation (EU) 2023/915. This sum includes ergometrine, ergosine, ergotamine, ergocornine, ergocryptine, and ergocristine together with their corresponding -inine epimers, increasing the demand for reliable analytical methods to support routine monitoring and enforcement. <a href="javascript:void(0);">(1,11)</a></p><p>Liquid chromatography-tandem mass spectrometry (LC-MS/MS), particularly ultrahigh performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), is widely regarded as the reference technique for confirmatory determination of ergot alkaloids due to its sensitivity, selectivity, and ability to resolve epimeric forms. Recent methods routinely achieve low microgram-per-kilogram limits of quantification across a range of cereal matrices. <a href="javascript:void(0);">(12−17)</a> However, LC-MS/MS approaches are resource-intensive and typically confined to centralized laboratories, limiting their suitability for high-throughput screening or rapid decision-making in grain-handling and quality-control settings. Consequently, rapid screening methods, most notably enzyme-linked immunosorbent assays (ELISAs), are commonly employed as complementary tools to chromatographic analysis. <a href="javascript:void(0);">(18−21)</a> ELISAs offer reduced analysis time, simplified workflows, and lower per-sample costs, making them attractive for preliminary screening and sample triage. <a href="javascript:void(0);">(22−24)</a></p><p>In contrast to other regulated mycotoxins, however, the commercial availability of ELISAs for ergot alkaloids is limited. While multiple kits have been evaluated, performance has varied substantially across assays and matrices. <a href="javascript:void(0);">(1)</a> At present, the Randox Food Diagnostics Ergot Alkaloids ELISA is the only widely marketed microplate ELISA that quantifies the sum of 12 major ergot alkaloids, comprising ergometrine, ergosine, ergotamine, ergocornine, ergocryptine, and ergocristine together with their corresponding -inine epimers, consistent with the analyte scope used for EU maximum levels for ergot alkaloids in specified cereal products. <a href="javascript:void(0);">(25)</a></p><p>In addition, cereal matrix effects may influence antibody binding and signal generation, potentially resulting in biased quantification relative to LC-MS/MS reference methods. These limitations are particularly relevant given the compositional variability of ergot alkaloids across cereal species, geographic regions, and growing conditions. <a href="javascript:void(0);">(12)</a> Recent reviews emphasize the need for systematic, matrix-specific evaluation of immunoassay performance before such methods can be confidently integrated into regulatory or industrial monitoring programs. <a href="javascript:void(0);">(1,6,11)</a> However, independent evaluations of commercially available ergot alkaloid ELISAs, particularly those benchmarked against validated UHPLC-MS/MS methods using naturally infested wheat samples, remain limited.</p><p>In this context, we hypothesized that measurements of total ergot alkaloids obtained using a commercially available ELISA are influenced by matrix effects and antibody cross-reactivity, resulting in systematic differences compared to UHPLC-MS/MS, which provides compound-specific quantification. To test this, the objective of the present study was to conduct a comprehensive performance evaluation of a commercially available ELISA for the detection of ergot alkaloids in wheat, using UHPLC-MS/MS as a reference method. Specific aims included assessment of repeatability and intermediate precision, extraction efficiency and extract stability, the influence of test portion mass, method accuracy relative to UHPLC-MS/MS, and characterization of antibody cross-reactivity toward individual ergot alkaloids in both solvent and wheat matrix. The results provide data-driven guidance on the appropriate use of ELISA-based screening within tiered analytical strategies for regulatory monitoring and food safety decision-making.</p><h4><strong>2. Materials and Methods</strong></h4><h5><strong>2.3. UHPLC-MS/MS Reference Method</strong></h5><p>UHPLC-MS/MS analysis of ergot alkaloids was performed using the validated Canadian Grain Commission (CGC) method described by Tittlemier et al. (2015). Briefly, ground grain (10 g) was extracted with 50 mL of acetonitrile/aqueous ammonium carbonate (84:16, v/v; 3.03 mM ammonium carbonate) to provide alkaline extraction conditions, then shaken for 30 min and centrifuged at 2450<i>g</i> for 10 min at room temperature. An aliquot of extract (464 μL) was combined with internal standard solution (dihydroergotamine; 20 μL of 4 ng/μL) and aqueous ammonium carbonate (1536 μL), vortex-mixed, and filtered through a 0.45 μm polytetrafluoroethylene syringe filter before injection into the UHPLC-MS/MS system. As in the validated reference method, dihydroergotamine was added after extraction to correct for postextraction analytical variability; extraction recovery was evaluated during method validation. Chromatographic separation was achieved using a reversed-phase <strong>BEH C18 column</strong> (2.1 × 100 mm, 1.7 μm; Waters, Milford, MA, USA) with the autosampler maintained at 15 °C and the column at 30 °C. Mobile phases consisted of (A) 3.03 mM aqueous ammonium carbonate and (B) acetonitrile. The gradient program was as follows: initial, 75% A/25% B; 1.00 min, 60% A/40% B; 5.00 min, 40% A/60% B; 8.00 min, 22% A/78% B; 10.50–11.00 min, 10% A/90% B; and 13.00–16.00 min, 75% A/25% B, with a total run time of 16 min. Detection was performed using positive electrospray ionization in multiple reaction monitoring mode on a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/554"><strong>Waters Xevo triple quadrupole mass spectrometer</strong></a> (Waters, Milford, MA, USA). Under the validated chromatographic conditions, dihydroergotamine did not coelute with ergotamine, ergotaminine, or the other target ergot alkaloids. Identification and quantification were based on retention-time criteria and compound-specific MRM transitions, thereby minimizing potential isotopic or coelution interference. Precautions to minimize epimerization, including controlled handling of standards and extracts and reduced light exposure, were followed as described in the reference method. UHPLC-MS/MS quantification was performed using analyte-specific, matrix-matched calibration curves prepared according to the validated CGC reference method, with calibration levels of 0.046, 0.2, 1, 2, 10, and 20 μg/kg. Dihydroergotamine was used as the internal standard, and concentrations were calculated from internal-standard-normalized analyte responses with method dilution factors applied. Total ergot alkaloid concentration was calculated as the arithmetic sum of all quantified ergot alkaloids and epimers included in the validated method. <a href="javascript:void(0);">(26)</a></p><h4><strong>3. Results and Discussion</strong></h4><h5><strong>3.4. Comparison of ELISA and UHPLC-MS/MS Results</strong></h5><p>For method comparison, UHPLC-MS/MS was used as the chemical reference method, providing compound-specific quantification of individual ergot alkaloids and their epimers. A total ergot alkaloid concentration was calculated as the arithmetic sum of all quantified alkaloids included in the method. This summed value represents a chemically defined total based on compound-specific quantification of each analyte, rather than an immunoreactivity-weighted response governed by antibody affinity. As such, the UHPLC-MS/MS total serves as a chemically defined comparator against which the immunoreactivity-weighted ELISA response can be interpreted. Agreement between the commercial ELISA and the validated UHPLC-MS/MS reference method was evaluated using wheat and durum wheat cargo samples (<i>n</i> = 102) collected over multiple crop years (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jafc.6c05234#fig5">Figure 5</a>). Linear regression analysis demonstrated a positive association between ELISA and UHPLC-MS/MS results across the full concentration range, indicating that the ELISA was responsive to increasing ergot alkaloid levels. However, the regression slope deviated substantially from unity, with ELISA results systematically lower than UHPLC-MS/MS values, indicating an approximate 2-fold underestimation.&nbsp;</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/J_Agric_Food_Chem_2026_74_25_20015_20027_Figure_5_Linear_regression_analysis_comparing_total_ergot_alkaloid_concentrations_determined_by_ELISA_and_UHPLC_MS_MS_5d7b5c5c61.jpeg" alt="J. Agric. Food Chem. 2026, 74, 25, 20015–20027: Figure 5. Linear regression analysis comparing total ergot alkaloid concentrations determined by ELISA and UHPLC-MS/MS for wheat and durum wheat cargo samples (n = 102). Each point represents the mean of duplicate measurements (extracted from the same test portion) ELISA determinations for an individual cargo sample, plotted against the corresponding UHPLC-MS/MS result. Statistical analysis was performed using linear regression." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_J_Agric_Food_Chem_2026_74_25_20015_20027_Figure_5_Linear_regression_analysis_comparing_total_ergot_alkaloid_concentrations_determined_by_ELISA_and_UHPLC_MS_MS_5d7b5c5c61.jpeg 197w," sizes="100vw" width="992" height="784"></p><p>Bland-Altman analysis confirmed this proportional bias, showing a consistent negative mean difference between ELISA and UHPLC-MS/MS results across the concentration range (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.jafc.6c05234#fig6">Figure 6</a>). Importantly, the magnitude of disagreement did not increase randomly with concentration; rather, it reflected a systematic offset, indicating that the discrepancy was not driven by analytical imprecision or outliers but by fundamental differences in method response characteristics. This pattern indicates method-level bias rather than random analytical variability, which may arise from combined workflow effects including extraction, matrix response, and immunochemical cross-reactivity. The magnitude of the ELISA-UHPLC-MS/MS bias was substantially greater than the intermediate precision observed for the ELISA quality-control material, supporting the interpretation that the disagreement reflects systematic differences in method response rather than insufficient ELISA repeatability. Such behavior is well documented when immunoassays are compared with chromatographic methods for complex mycotoxin mixtures, including ergot alkaloids and other structurally diverse mycotoxins in cereals and feed. <a href="javascript:void(0);">(28,30,33)</a> These studies consistently report matrix- and profile-dependent bias in ELISA relative to LC-MS/MS, arising from differential antibody cross-reactivity and the summed immunoreactivity response of the assay, because ELISA produces an immunoreactivity-weighted total that depends on antibody affinity toward individual alkaloids and their relative abundance in the sample, whereas UHPLC-MS/MS quantifies compound-specific concentrations of each alkaloid and its epimers using compound-specific transitions and response factors, and total ergot alkaloid concentration is calculated as the sum of these targeted analytes. In contrast, ELISA produces an immunoreactivity-weighted total, determined by antibody affinity toward individual alkaloids and their competitive binding behavior within the assay format. Consequently, agreement between ELISA and UHPLC-MS/MS depends not only on total concentration, but also on the relative distribution of individual alkaloids within each sample. Although differences in extraction solvent composition and pH may influence ergot alkaloid recovery, stability, and epimeric distribution, each method was applied according to its intended analytical workflow. The ELISA was performed using the manufacturer-recommended acidic methanol/water extraction, whereas UHPLC-MS/MS was performed using the validated acetonitrile/aqueous ammonium carbonate extraction procedure. Therefore, the comparison reflects the performance of the complete methods as used in practice, rather than an isolated comparison of extraction solvents. The sequential extraction experiment further showed that repeating the ELISA extraction under the same kit conditions did not substantially increase the ELISA-measured response, supporting the adequacy of the kit extraction within the ELISA workflow while recognizing that it does not directly compare acidic and ammonium carbonate-based extraction conditions. Previous ELISA-LC-MS/MS comparison studies for ergot alkaloids have reported both under- and overestimation depending on assay design and matrix, including differences in alkaloid profile, cereal type, and antibody cross-reactivity. Turner et al. observed substantial overestimation of ergot alkaloids by ELISA relative to HPLC in rye field samples, attributed to strong antibody cross-reactivity toward alkaloids prevalent in rye matrices. Similar profile-dependent bias has also been reported in interlaboratory and method-comparison studies, <a href="javascript:void(0);">(33)</a> demonstrating that this behavior is not unique to a single data set.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/J_Agric_Food_Chem_2026_74_25_20015_20027_Figure_6_Bland_Altman_plot_comparing_ELISA_and_UHPLC_MS_MS_measurements_of_total_ergot_alkaloids_1be40cce50.jpeg" alt="J. Agric. Food Chem. 2026, 74, 25, 20015–20027: Figure 6. Bland-Altman plot comparing ELISA and UHPLC-MS/MS measurements of total ergot alkaloids for wheat and durum wheat cargo samples (n = 102)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_J_Agric_Food_Chem_2026_74_25_20015_20027_Figure_6_Bland_Altman_plot_comparing_ELISA_and_UHPLC_MS_MS_measurements_of_total_ergot_alkaloids_1be40cce50.jpeg 230w," sizes="100vw" width="1437" height="977"></p><p>This study provides a comprehensive evaluation of a commercially available ELISA for total ergot alkaloids, using wheat samples as the primary application matrix, and integrates performance metrics with mechanistic insights into method behavior. While the assay demonstrated strong repeatability, calibration stability, and robustness to procedural factors such as test portion mass and extraction conditions, systematic differences relative to UHPLC-MS/MS were consistently observed. By linking these differences to compound-specific antibody cross-reactivity and matrix-dependent signal modulation, this work clarifies that ELISA-derived results reflect an immunochemically weighted response rather than a stoichiometric total. This distinction is critical for the appropriate interpretation of ELISA data and supports its use within tiered analytical strategies as a rapid screening tool, complemented by UHPLC-MS/MS for confirmatory quantification and regulatory decision-making.</p></div>

Comparative Evaluation of Total Ergot Alkaloids Determination by ELISA and UHPLC-MS/MS in Wheat: Implications of Cross-Reactivity and Matrix Effects

<p><strong>In the week of July 6, the following webinars await you in the field of liquid phase and especially HPLC and LC/MS.</strong></p><blockquote><h4><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinars"><strong>👉 DETAILS AND REGISTRATION IN THE WEBINARS SECTION</strong></a></h4><p><strong>👉 Search and filter in the largest global database</strong> with over <strong>5 500 GC, LC, MS and spectroscopy webinars</strong>.</p></blockquote><h5><strong>1. Waters Corporation: Characterizing Next-Generation Antibody Therapeutics: LC Strategies for Multispecifics, ADCs &amp; AOCs</strong></h5><ul><li>Tu, 7.7.2026 11:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6317">Registration</a></li></ul><p>In this webinar, we share a pragmatic characterization roadmap using LC-based methods across intact, subunit, and peptide-mapping workflows.</p><h5><strong>2. Separation Science: Advances in Antibiotic Extraction from Water: An Automated SPE Approach</strong></h5><ul><li>We, 8.7.2026 09:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6319">Registration</a></li></ul><p>Streamline water analysis workflows and gain practical insights for modern environmental monitoring.</p><h5><strong>3. SCIEX: Analysis of per- and polyfluoroalkyl substances (PFAS) in food substances using LC-MS/MS solutions</strong></h5><ul><li>We, 8.7.2026 15:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6322">Registration</a></li></ul><p>Master PFAS analysis in food safety. Learn how SCIEX LC-MS/MS solutions and QTRAP workflows overcome analytical challenges to ensure accurate and compliant result confirmation.</p><h5><strong>4. Wiley: From liquids to solids: expand what your UV-Vis-NIR Spectrometer can do</strong></h5><ul><li>We, 8.7.2026 16:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6367">Registration</a></li></ul><p>Discover how the Agilent Cary UV-Vis-NIR spectrometer, together with Specac accessories, enables reliable analysis of liquids, powders, films, pellets, and highly scattering solid samples.</p><h5><strong>5. Thermo Fisher Scientific: Advanced tools to maximize your sample throughput with Chromeleon Software and Vanquish UHPLC</strong></h5><ul><li>Th, 9.7.2026 11:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6326">Registration</a></li></ul><p>Learn how Chromeleon software and the Vanquish Duo UHPLC system streamline sample analysis, automate routine workflows, increase throughput, and reduce errors through practical demonstrations.</p><h5><strong>6. Bruker: 4D-Metabolomics™ in Action: Real-World Strategies for Deep Discovery and Confident Annotation</strong></h5><ul><li>Th, 9.7.2026 17:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6328">Registration</a></li></ul><p>Explore how next-generation mass spectrometry technologies, ion mobility, and computational tools are helping researchers move from complex datasets to confident insight.</p><h5><strong>7. Waters Corporation: Cracking the Code on Nitrogen Methods</strong></h5><ul><li>Th, 9.7.2026 17:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6327">Registration</a></li></ul><p>Learn the fundamentals of nitrogen analysis for wastewater testing. Explore analytical methods, QA/QC, sample handling, compliance reporting, and troubleshooting for accurate environmental monitoring.</p><h5><strong>8. SelectScience: Next-generation metabolomics: From annotation to discovery at scale</strong></h5><ul><li>Th, 9.7.2026 17:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6281">Registration</a></li></ul><p>Explore how next-generation mass spectrometry, ion mobility, and advanced computational tools accelerate confident small-molecule annotation and discovery in metabolomics.</p><h5><strong>9. SCIEX: LC-MS/HRMS Approaches for Monitoring Organic Micropollutants in Wastewater and Environmental Systems</strong></h5><ul><li>Fr, 10.7.2026 15:00 CEST</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/6370">Registration</a></li></ul><p>Discover how advanced LC-MS/HRMS workflows enable trace-level detection of organic micropollutants, suspect and non-target screening, and environmental monitoring of wastewater systems.</p>

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Thermo Scientific™ Dionex™ Inuvion™ Core ion chromatography system

The Inuvion Core system gives you all the benefits of chemical suppression and higher-pressure operation, with manual eluent preparation.

<h3><strong>Welcome to the evolution of everyday IC reliability</strong></h3><p>The new<strong> Thermo Scientific™ Dionex™ Inuvion™ ion chromatography system</strong> makes ion analysis simpler and more intuitive than ever before. And it delivers exactly what a busy analytical testing lab is looking for: <strong>consistently excellent results-every shift, every day, for every operator.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Dionex_Inuvion_ion_chromatography_system_2_6400708696.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ ion chromatography system." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Dionex_Inuvion_ion_chromatography_system_2_6400708696.jpg 245w," sizes="100vw" width="825" height="498"></p><h3><strong>Start with Inuvion Core</strong></h3><p>The <strong>Inuvion Core system</strong> gives you<strong> </strong>all the benefits of chemical suppression and higher-pressure operation, with manual eluent preparation. You still enjoy the<strong> same robust Dionex Inuvion platform</strong>-easily configurable and economically upgradeable to full-featured capabilities as budget allows.</p><figure class="image"><img style="aspect-ratio:650/650;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Dionex_Inuvion_Core_ion_chromatography_system_6c8824cb1d.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ Core ion chromatography system." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Dionex_Inuvion_Core_ion_chromatography_system_6c8824cb1d.jpg 156w," sizes="100vw" width="650" height="650"></figure><h3><strong>SIMPLE, INTUITIVE USER EXPERIENCE&nbsp;</strong></h3><ul><li><strong>Smart, function-driven design</strong> lets you quickly and safely access everything on the instrument—no hard-to-reach compartments, and no step stools or extra tools needed!</li><li><strong>Automated startup and shutdown routines</strong> ensure the system is quickly ready for the day’s work without user intervention.&nbsp;</li><li><strong>Built-in how-to videos</strong> reduce training time and simplify setup and operation.</li></ul><h3><strong>ULTRA-RELIABLE PERFORMANCE&nbsp;</strong></h3><ul><li><strong>Advanced high-performance pump technology and electronics</strong> let you take advantage of a wider range of columns and chemistries to improve the speed and quality of your results.</li><li><strong>Fast, flexible, convenient electrolytic suppression: </strong>Just connect the suppressor; no external pump or offline conditioning needed for regeneration.</li><li><strong>Reagent-free IC (RFIC™) capability</strong> makes eluent preparation as simple as “just add water,” while ensuring more consistent results and enabling optimized gradient separations.</li></ul><h3><strong>EASILY CONFIGURABLE AND UPGRADEABLE</strong></h3><ul><li><strong>Versatile, adaptable platform</strong> lets you configure the exact Dionex Inuvion IC system for today’s needs and budget, with confidence that your system will also meet your future needs.</li><li><strong>Multiple options and peripherals </strong>extend IC capabilities, letting you easily—and cost-effectively—adapt to changing sample types and workflow requirements.</li></ul><h3><strong>Simply the best system for everyday ion analysis</strong></h3><figure class="image"><img style="aspect-ratio:1107/755;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Dionex_Inuvion_ion_chromatography_system_d855feb2a8.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ ion chromatography system." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Dionex_Inuvion_ion_chromatography_system_d855feb2a8.jpg 229w," sizes="100vw" width="1107" height="755"></figure><p><strong>1. Operator-friendly engineering </strong>saves time and reduces errors by allowing easy, unobstructed access to all components, connections and consumables</p><p><strong>2. Compact design </strong>helps you make the most of valuable bench space</p><p><strong>3. Digital gas pressure regulator </strong>increases precision of gas delivery for maximum day-to-day consistency (optional)</p><p><strong>4. Temperature-controlled conductivity cell </strong>improves reproducibility and ensures baseline stability</p><p><strong>5. Vacuum degassing capability</strong> enables more consistent peak identification from smoother baselines</p><p><strong>6. Seal wash pump</strong> reduces maintenance costs when using manually prepared eluents (optional)&nbsp;</p><p><strong>7. Reagent-free IC (RFIC)</strong> saves time and ensures greater day-to-day and operator-to-operator consistency, while also allowing the use of gradient separations</p><p><strong>8. Electrolytic suppression</strong> entirely eliminates the need for manual regenerant preparation (or, opt for a continuously regenerated, always- ready-to-go chemical suppressor)</p><p><strong>9. Thermo Scientific™ Dionex™ IC PEEK Viper™ fittings</strong> ensure confident, low dead volume connections every time—no tools required! (optional)</p><p><strong>10. Integrated column heater</strong> minimizes the impact of fluctuations in lab temperature that can adversely affect results (optional)</p><p><strong>11. 6- or 10-port auxiliary valve</strong> lets you automate in-line sample preparation</p><p><strong>12. State-of-the-art high-pressure pump (up to 5000 psi)</strong> lets you increase flow rates with smaller particle columns to reduce run times or add additional separation capacity with longer column length</p><p><strong>13. System self-diagnostics </strong>automatically detect any issues with hardware and consumables</p><p><strong>14. Self-service capabilities and user-swappable parts</strong> help you get back up and running in a hurry Automatic eluent monitor alerts the operator to low solution levels, avoiding potential system damage or failed runs (optional)</p><p><strong>15. Automatic eluent monitor </strong>alerts the operator to low solution levels, avoiding potential system damage or failed runs (optional)</p><h3><strong>Flexible, adaptable Dionex Inuvion platform</strong></h3><p>You can <strong>configure your Dionex Inuvion system</strong> to meet specific analytical and budget requirements, and easily reconfigure as needed. Multiple configurations and peripherals extend IC capabilities, letting you easily-and cost-effectively-adapt to changing sample types and workflow requirements.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Dionex_Inuvion_ion_chromatography_system_3_fa8233bcd4.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ ion chromatography system." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Dionex_Inuvion_ion_chromatography_system_3_fa8233bcd4.jpg 245w," sizes="100vw" width="1246" height="572"></p><h3><strong>Consistently excellent results every day</strong></h3><p>The <strong>Dionex Inuvion IC system supports a full range of columns </strong>to improve the speed and quality of results, for both<strong> anions and cations.</strong> Expanded capabilities, such as Reagent-Free IC (RFIC), enhance operator-to-operator consistency, while enabling the use of eluent gradients to optimize separations.</p><h4><strong>Rapid results</strong></h4><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Pragolab_Obr_2_Ukazka_rychle_separace_zakladnich_aniontu_s_uhlicitanovou_MF_Zkraceni_doby_analyzy_diky_typu_kolony_a_vyssimu_prutoku_0e610b919d.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ Core ion chromatography system: Figure 1. Elution of seven common inorganic anions using carbonate eluent. Short columns and fast flow rates let you reduce run times." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Pragolab_Obr_2_Ukazka_rychle_separace_zakladnich_aniontu_s_uhlicitanovou_MF_Zkraceni_doby_analyzy_diky_typu_kolony_a_vyssimu_prutoku_0e610b919d.jpg 245w," sizes="100vw" width="1622" height="739"></p><h4><strong>Exceptional reproducibility</strong></h4><figure class="image"><img style="aspect-ratio:1693/754;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Pragolab_Obr_3_Ukazka_reprodukovatelnosti_analyzy_zakladnich_aniontu_40_nastriku_Spickova_technologie_cerpadla_a_elektronika_pristroje_poskytuji_konzistentni_a_reprodukovatelne_vysledky_f66e7430cf.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ Core ion chromatography system: Figure 2. Overlay of 40 replicate injections. State-of-the-art pump technology and Electronics deliver consistent, reproducible results." width="1693" height="754"></figure><h4><strong>Increased sensitivity and consistency</strong></h4><figure class="image"><img style="aspect-ratio:1860/836;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Pragolab_Obr_4_Ukazka_vysoce_citlive_analyzy_aniontu_ve_vodach_Eluent_generator_KOH_a_elektrolyticka_suprese_snizuji_pozadi_cimz_dochazi_ke_zvyseni_citlivosti_da55facfd0.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ Core ion chromatography system: Figure 3. Determination of inorganic anions in drinking and surface waters. KOH eluent generation and electrolytic suppression yield lower backgrounds for greater sensitivity and increased day-to-day consistency." width="1860" height="836"></figure><h4><strong>Method optimization</strong></h4><figure class="image"><img style="aspect-ratio:1799/889;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Pragolab_Obr_5_Ukazka_optimalizace_metody_zkraceni_doby_analyzy_pouzitim_gradientu_mobilni_faze_fc1fbe9cb0.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ Core ion chromatography system: Figure 4. Comparison of isocratic and gradient runs using eluent generation. Reduce run length and sharpen later-eluting peaks with the same ease as an isocratic run with no need for two separate eluents or a proportioning pump." width="1799" height="889"></figure><h3><strong>Compliance-ready Chromeleon CDS</strong></h3><p>A trusted industry standard all over the world, ”Simply Intelligent”<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong>Thermo Scientific™ Chromeleon™ Chromatography Data System (CDS) software </strong></a>brings out the full power of the Dionex Inuvion IC system. Easy to learn and easy to use, it automates and optimizes daily tasks and helps even inexperienced users achieve consistent, high quality results.</p><p><img style="aspect-ratio:3700/1660;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Thermo_Scientific_Dionex_Inuvion_2_303a6eb73b.jpg" alt="Thermo Scientific™ Dionex™ Inuvion™ Core ion chromatography system." width="3700" height="1660"></p>

Thermo Scientific™ ProSightPD Software

Perform comprehensive analysis of top-down proteomics data with Thermo Scientific™ ProSightPD™ software.

<div container-id="cq-colctrl-lt8" comp-id="B1"><div><h3><strong>Confident proteoform identification and characterization</strong></h3></div></div><div container-id="cq-colctrl-lt8" comp-id="B2"><div><p><strong>Uncover and confidently characterize proteoforms within complex matrices, including proteoforms containing truncations, alternative splices, and post-translationally modified proteins.</strong>&nbsp;</p><p>Extensive searches make use of <strong>various fragmentation methodologies (e.g., ETD, HCD, UVPD)</strong>, allowing you to make full use of the high-quality <strong>MS/MS data</strong> obtained when searching against the<strong> full biological complexity present in UniProt. </strong>With<strong> Thermo Scientific ProSightPD software, </strong>see what is really there and make the most of your data.</p><div><h3><strong>Key benefits</strong></h3><h5><strong>Sophisticated tools at your fingertips</strong></h5><p><strong>Utilize several search modes</strong> for identifying intact and truncated proteins. ProSightPD software offers the ability to search entire raw files or quickly select specific MS<sup>2</sup> scans for further searching. Information in UniProt enables the identification of modified or processed proteins.</p><h5><strong>Remove the guesswork from database management</strong></h5><p><strong>Import result files </strong>from<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1782"><strong> Proteome Discoverer</strong></a><strong> software</strong> or entire proteomes via UniProt formatted XML and FASTA files with Database Manager. Fully customize imported databases using thr<strong> ProSight Annotator GUI </strong>to characterize PTMs, disulfide bonds, mutations and truncations.</p><h5><strong>Intuitive user interface</strong></h5><p><strong>Analyze large datasets</strong> with many data files using <strong>ProSightPD nodes for </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1782"><strong>Proteome Discoverer</strong></a><strong> software. </strong>Create multi-step searches and utilize built in results interpretation tools.</p><h3><strong>Search Types</strong></h3><div><p><strong>Different database search modes</strong> allow you to optimize data interrogation based upon your experimental needs. Searches are driven through the use of a node-based system allowing flexibility of experimental design.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Pro_Sight_PD_Software_8a96430534.jpeg" alt="Thermo Scientific™ ProSightPD Software: ProSightPD Database Searching." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Pro_Sight_PD_Software_8a96430534.jpeg 245w," sizes="100vw" width="960" height="540"></p><div><p>Further information relating to the two search modes, Absolute Mass Search and Biomarker Search.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Pro_Sight_PD_Software_2_01f6c31076.jpeg" alt="Thermo Scientific™ ProSightPD Software: Complementary Search Types: Digging Deeper in Complex Samples." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Pro_Sight_PD_Software_2_01f6c31076.jpeg 245w," sizes="100vw" width="960" height="540"></p><h3><strong>Database Management</strong></h3><div><p><strong>Confident proteoform identification </strong>is realized through the use of XML-formatted databases, ensuring that nothing is missed.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Pro_Sight_PD_Software_3_db19f0cee9.jpeg" alt="Thermo Scientific™ ProSightPD Software: Database Manager: Add remove isoforms and PTMs." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Pro_Sight_PD_Software_3_db19f0cee9.jpeg 245w," sizes="100vw" width="960" height="540"></p><div><p><strong>Improvements to data visualization</strong> ensure that you can better interact with and interpret your data, minimizing the time taken to deliver actionable results.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Pro_Sight_PD_Software_4_575aa9dff5.jpeg" alt="Thermo Scientific™ ProSightPD Software: LFQ Visualizations." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Pro_Sight_PD_Software_4_575aa9dff5.jpeg 245w," sizes="100vw" width="960" height="540"></p><h3><strong>ProSightPD nodes</strong></h3><p><strong>Top-Down Workflows:</strong> ProSightPD&nbsp;includes templates to easily build the most commonly used-top down data analysis workflows.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Pro_Sight_PD_Software_5_4f28a7434d.jpg" alt="Thermo Scientific™ ProSightPD Software: ProSightPD 2.0: Tailored Workflows for All Types of Data." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Pro_Sight_PD_Software_5_4f28a7434d.jpg 245w," sizes="100vw" width="740" height="400"></p></div></div></div></div></div></div></div>

Thermo Scientific™ Mass Frontier™ Spectral Interpretation Software

Transform your mass spectral data into knowledge quickly and easily using Thermo Scientific™ Mass Frontier™ spectral interpretation software. 

<p><strong>Transform your mass spectral data into knowledge quickly and easily using Thermo Scientific™ Mass Frontier™ spectral interpretation software. Take the challenge out of small molecule structural elucidation for metabolism, metabolomics, forensics, natural products, impurities, and degradants studies.</strong></p><p><strong>High-quality, curated experimental spectral and fragmentation libraries</strong> simplify the deconvolution, evaluation, interpretation and management of infusion, and LC, nominal mass, or high resolution mass spectral data. Streamline building and curating your library and sharing it with your colleagues and collaborators. <strong>Mass Frontier software complements Thermo Scientific™ </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer™</strong></a><strong> software</strong> for routine-based small molecule discovery and identification.</p><h3><strong>See what's really there</strong></h3><ul><li>Deconvolute your nominal mass or high resolution LC-MS<sup>n</sup> or infusion data.</li><li>Capture all of your data, no matter how complex, with simple interrogation of all components.</li></ul><h3><strong>Know more unknowns</strong></h3><ul><li><strong>Transform </strong>your small molecule unknown data into actionable knowledge.</li><li><strong>Search </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud™</strong></a><strong> mass spectral library</strong>, the world's most comprehensive and structurally diverse fully curated mass spectral database.</li><li><strong>Maximize the utility of your MS<sup>n</sup> data</strong> for the confident identification of unknown with spectral tree searching.</li><li><strong>Enhance your confidence</strong> in proposed unknown candidate structures by using <strong>Thermo Scientific™ </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1762"><strong>mzLogic™</strong></a><strong> algorithm</strong>, based on similarity searching to millions of fragment annotated spectra.</li></ul><figure class="image"><img style="aspect-ratio:740/405;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_3_167df5dc63.jpg" alt="Thermo Scientific™ Mass Frontier™ Spectral Interpretation Software: mzCloud mass spectral library." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_3_167df5dc63.jpg 245w," sizes="100vw" width="740" height="405"></figure><h3><strong>Go from spectra to structure</strong></h3><ul><li>The HighChem Fragmentation Library™ includes <strong>&gt;54,000 fragmentation schemes, ∼ 220,000 individual reactions, and 256,000 chemical structures</strong>, all from peer-reviewed literature.</li><li>Spectral trees are fully annotated with fragmentation structures.</li><li><strong>FISh (fragment ion search) detection</strong> enables detection of structurally related compounds, indicating the site of transformations for drug metabolites.</li></ul><figure class="image"><img style="aspect-ratio:740/350;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_2_37f024ef32.jpg" alt="Thermo Scientific™ Mass Frontier™ Spectral Interpretation Software" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_2_37f024ef32.jpg 245w," sizes="100vw" width="740" height="350"></figure><h3><strong>Build your pathways</strong></h3><ul><li>Interactively search more than <strong>370 curated</strong> <strong>biochemical pathways</strong> with<strong> Thermo Scientific™ Metabolika™</strong> pathway mapping.</li><li>Create and understand fragmentation pathways and mechanisms using advanced fragmentation scheme knowledge base drawn from more than 99% of published fragmentation pathways.</li></ul><figure class="image"><img style="aspect-ratio:740/410;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_4_7d1b4f8671.jpg" alt="Thermo Scientific™ Mass Frontier™ Spectral Interpretation Software: An example of an included Metabolika biological pathway, which can be fully edited and added to." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_4_7d1b4f8671.jpg 245w," sizes="100vw" width="740" height="410"></figure><h3><strong>Store, share and utilize your knowledge</strong></h3><ul><li><strong>Translate your data into actionable knowledge:</strong> create, curate and store your own spectral libraries and pathways.</li><li><strong>Ensure the highest quality proprietary libraries</strong> with full curation and mass recalibration tools.</li></ul><figure class="image"><img style="aspect-ratio:740/345;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_5_e89924a0b7.jpg" alt="Thermo Scientific™ Mass Frontier™ Spectral Interpretation Software: The new curator module automates spectral tree curation, fragment annotation and mass recalibration for your proprietary compounds to build a high quality curated local MSn library." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Mass_Frontier_Spectral_Interpretation_Software_5_e89924a0b7.jpg 245w," sizes="100vw" width="740" height="345"></figure>

Thermo Scientific Xcalibur Software

Confidently control, acquire, and interrogate data from a range of Thermo Scientific LC-MS systems and related instruments using Thermo Scientific Xcalibur software.

<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 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>

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