<p><strong>Join us for a fascinating conversation with Dr. Subhoja Chakraborty from the University of Central Florida, whose cutting-edge research targets the global challenge of malaria drug resistance. Dr. Chakraborty shares her journey from structure-based drug design during her PhD to her recent collaborative work repurposing human kinase inhibitors as rapid, selective antimalarials against drug-resistant Plasmodium falciparum strains.</strong></p><h4><strong>In this episode, you'll learn:</strong></h4><ul><li>How structure-guided approaches reveal potential drug targets, including cysteine proteases like falcipain-2, and kinases implicated in malaria's complex life cycle.</li><li>The power of repurposing kinase inhibitors originally developed for cancer and other diseases, focusing on compound 12, which blocks hemozoin formation and protein kinase 6—key steps in parasite survival.</li><li>Lab techniques such as affinity, gel filtration, and size exclusion chromatography for recombinant protein purification—and how troubleshooting is crucial for high-yield, stable complexes.</li><li>Advances in mass spectrometry for characterizing protein interactions, validating drug targets, and mapping molecular pathways pivotal to malaria therapeutics.</li><li>Tips and lessons for new researchers facing the challenges of sample preparation, complex protocols, and working as part of a collaborative team.</li></ul><p>Dr. Chakraborty’s insights bridge the gap between basic science and translational drug discovery, offering hope for more effective, targeted malaria treatments in a world where resistance to frontline therapies threatens millions.</p><h4><strong>Referenced Papers:</strong></h4><ul><li>"Plasmodium falciparum protein kinase 6 and hemozoin formation are inhibited by a type II human kinase inhibitor exhibiting antimalarial activity" (Cell Chemical Biology, 2025)</li><li>"New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain" (BBRC, 2022)</li><li>"Structure-Based Optimization of Protease−Inhibitor Interactions to Enhance Specificity of Human Stefin‑A against Falcipain‑2 from the Plasmodium falciparum 3D7 Strain" (Biochemistry, 2023)</li></ul><p>If you’re a student, scientist, or simply passionate about advances in infectious disease research, this episode offers actionable insights, inspiring advice, and a front-row seat to innovation in combating malaria.</p><h3><strong>Video Transcription</strong></h3><h4><strong>From Structural Biology to Drug Discovery: Chromatography and Mass Spectrometry in Malaria Research</strong></h4><h5><strong>Introduction</strong></h5><p>In this discussion, Subhoja shares insights into her research journey, focusing on malaria drug discovery and the role of modern analytical techniques in biological and biomedical research. The conversation is aimed primarily at undergraduate students and early-career researchers interested in chemistry, biotechnology, and life sciences.</p><h5><strong>Research Focus: Malaria Drug Discovery and Kinase Targets</strong></h5><p>Subhoja is currently involved in malaria drug discovery research at the University of Central Florida, where she has been working since beginning her postdoctoral position two years ago. Her earlier PhD research focused on structure-based drug design in malaria, using a combination of in silico approaches, recombinant protein expression, and X-ray crystallography to determine precise three-dimensional structures of target proteins and their inhibitors.</p><p>This structural perspective provided a foundation for her current work, which centers on drug discovery through compound screening and repurposing. A recent publication from her laboratory explores the use of repurposed mammalian CDK-like kinase inhibitors as potential antimalarial agents. While such kinase inhibitors are well known in cancer and cardiovascular research, their application to malaria targets represents a novel and promising approach.</p><p>Kinases are attractive drug targets because of their central role in cell signaling and growth pathways. By targeting specific kinases involved in different stages of the malaria parasite life cycle—whether asexual growth, gametocytogenesis, or differentiation—it may be possible to significantly inhibit parasite growth and progression.</p><h5><strong>Chromatography in Protein Expression and Purification Workflows</strong></h5><p>Chromatography plays a critical role throughout Subhoja’s research. Her experience spans from basic chromatography techniques during her early training to advanced protein purification workflows using affinity chromatography, gel filtration (size exclusion chromatography), and ion exchange chromatography.</p><p>Recombinant proteins are routinely purified using affinity resins such as nickel or cobalt, followed by further purification to remove contaminants. Fast Protein Liquid Chromatography (FPLC) enables compact, stepwise purification workflows suitable for producing proteins for in vitro assays.</p><p>A recurring challenge in this process is the expression of high-molecular-weight proteins, which often accumulate in insoluble fractions or inclusion bodies. Careful selection of expression vectors, host systems, and induction conditions is therefore essential to maximize yield and solubility.</p><h5><strong>Integrating Size Exclusion Chromatography into the Workflow</strong></h5><p>Size exclusion chromatography (SEC) is typically used after affinity purification to further improve protein purity. Following elution with imidazole or glutathione, desalting is required to prevent buffer components from interfering with downstream assays. This is often achieved using desalting columns such as G-25 or PD-10.</p><p>To remove lower-molecular-weight contaminants, finer SEC media—such as Superdex or Sephacryl columns—are employed. Concentration steps using molecular-weight cut-off filters are then applied to obtain the desired protein concentration for functional studies.</p><p>These iterative purification and troubleshooting steps are a routine part of protein biochemistry and reflect the importance of methodical optimization and careful validation.</p><h5><strong>The Role of Mass Spectrometry in Biomolecular Characterization</strong></h5><p>Mass spectrometry is a key analytical tool in Subhoja’s research pipeline, particularly for target identification and validation. In both malaria and cancer research, MS is used alongside chromatography, immunoprecipitation, and pull-down assays to study protein interactions and molecular recognition events.</p><p>Affinity-based mass spectrometry enables the identification of binding partners and interactors, whether studying proteins, long non-coding RNAs, or protein complexes. Techniques such as native MS, tandem affinity purification, and proximity labeling (e.g., TurboID-based workflows) provide deeper insights into molecular networks and signaling pathways.</p><p>These approaches are essential for understanding how candidate drug targets function within complex biological systems.</p><h5><strong>Sample Preparation Challenges in Biological Research</strong></h5><p>Sample preparation remains one of the most challenging aspects of biological experimentation. Whole-cell lysates contain proteases, nucleases, and other components that can rapidly degrade target molecules. Preventing degradation requires minimizing preparation time, maintaining low temperatures, and using appropriate inhibitor cocktails.</p><p>Reproducibility is also critical: biological experiments require multiple replicates, and variability is often unavoidable. Careful handling, protocol optimization, and continuous troubleshooting are essential to ensure reliable results, whether preparing samples for chromatography, mass spectrometry, sequencing, or immunoprecipitation.</p><h5><strong>Advances in Chromatography and MS for Malaria Research</strong></h5><p>Modern advances in chromatography and mass spectrometry significantly enhance malaria research by enabling precise target identification, quantification, and functional characterization. Drug discovery workflows begin with construct design and recombinant expression, followed by purification and interaction studies.</p><p>In malaria research, stage-specific parasite biology requires careful extraction and analysis of proteins from different life cycle stages. Tandem affinity MS, immunoprecipitation, and in vivo validation studies help confirm target relevance and therapeutic potential.</p><p>Recent work on repurposed kinase inhibitors has shown promising results, including inhibition of hemozoin formation—a key detoxification pathway for the malaria parasite—highlighting the potential of such compounds for further development.</p><h5><strong>Malaria, Drug Resistance, and Global Impact</strong></h5><p>Malaria remains a major global health burden, with over 600,000 deaths annually and widespread drug resistance complicating treatment. Artemisinin resistance, particularly associated with mutations in the K13 propeller domain, has driven the search for new targets and therapies.</p><p>During her PhD, Subhoja focused on falcipain-2, a cysteine protease involved in hemoglobin degradation within the parasite. This pathway is critical for parasite survival and has emerged as a promising drug target. Her work revealed that falcipain-2 operates within a larger protein complex responsible for hemoglobin processing and amino acid release.</p><p>Understanding these molecular mechanisms is essential for developing robust, stage-specific antimalarial strategies.</p><h5><strong>Advice for Early-Career Researchers</strong></h5><p>For researchers just starting out, Subhoja emphasizes the importance of hands-on experience. Working directly with cells, lysates, and analytical tools is essential for truly understanding experimental systems. Failure is an inherent part of research, and perseverance is key.</p><p>Motivation, teamwork, careful sample handling, and thorough preparation all contribute to long-term success. Reading extensively, critically evaluating one’s own work, and appreciating incremental progress are vital aspects of a sustainable research career.</p><p>Every successful experiment—no matter how small—represents meaningful progress and contributes to the broader goals of science and medicine.</p><h5><strong>Closing Remarks</strong></h5><p>The discussion highlights how interdisciplinary approaches combining chromatography, mass spectrometry, structural biology, and biochemistry are driving advances in malaria drug discovery. Through careful experimental design, analytical rigor, and collaborative teamwork, researchers can address complex biological challenges and contribute to global health solutions.</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>

Affinity, Gel Filtration, Size Exclusion Chromatography: Repurposing Kinase Inhibitors for Malaria

<p><strong>In the week of February 9, 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>5 000 GC, LC, MS and spectroscopy webinars</strong>.</p></blockquote><h5><strong>1. SelectScience: High-Throughput Stability Screening Strategies for Antibody Formulation</strong></h5><ul><li>Tu, 10.2.2026 17:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5807">Registration</a></li></ul><p>Learn how high-throughput DLS/SLS and rapid-screening DSC accelerate stability assessment of high-concentration antibody formulations, enabling faster, data-driven biologics development.</p><h5><strong>2. Phenomenex: Big Scale, Big Wins – Prep Chromatography Explained</strong></h5><ul><li>We, 11.2.2026 10:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5793">Registration</a></li></ul><p>Learn how to scale analytical methods to preparative HPLC, optimize loading capacity, and understand the limits of preparative columns for pharmaceutical applications.</p><h5><strong>3. ALS Czech Republic: PFAS in Food &amp; Food Contact Material</strong></h5><ul><li>We, 11.2.2026 15:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5816">Registration</a></li></ul><p>Get a practical overview of PFAS in food and food contact materials, including EU and US regulations, key analytical challenges, and reliable PFAS testing strategies.</p><h5><strong>4. New Food Magazine: The Science of Next-Gen Ingredients – Fermentation, Formulation and Function</strong></h5><ul><li>We, 11.2.2026 16:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5720">Registration</a></li></ul><p>Explore how fermentation-driven innovation is transforming functional food ingredients and how advanced analytics optimize flavour, functionality, and stability.</p><h5><strong>5. SCIEX: Accurate Mass Fundamentals – Interpreting and Applying Your Data</strong></h5><ul><li>We, 11.2.2026 19:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5772">Registration</a></li></ul><p>Session 3 focuses on interpreting and applying accurate mass data to confirm compound identity, move beyond basic quantitation, and troubleshoot results for confident reporting.</p><h5><strong>6. Agilent Technologies: Process Analytical Techniques – Online HPLC for Real-Time Monitoring and Control of Bioprocesses</strong></h5><ul><li>Th, 12.2.2026 06:30 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5834">Registration</a></li></ul><p>Discover how PAT HPLC enables near-real-time monitoring of critical quality attributes in bioprocessing, with a case study on charge-variant control by cation-exchange chromatography.</p><h5><strong>7. Thermo Fisher Scientific: Introducing the Orbitrap Excedion Pro Hybrid MS</strong></h5><ul><li>Th, 12.2.2026 11:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5889">Registration</a></li></ul><p>Discover the new Orbitrap Exploris Pro with expanded ETD/EThcD capabilities for confident biopharmaceutical characterization, including intact proteins, PTMs, ADCs, and large biomolecules.</p><h5><strong>8. Waters Corporation: Planning Your NuGenesis Upgrade – Insights and Best Practices for a Smooth Transition</strong></h5><ul><li>Th, 12.2.2026 19:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5833">Registration</a></li></ul><p>Learn how to plan a successful NuGenesis upgrade, transition to Windows 11, and unlock new capabilities such as dashboards for real-time operational insights.</p><h5><strong>9. Thermo Fisher Scientific: Comprehensive Analytical Strategies for Peptide Therapeutics and GLP-1 Agonists with Agilent</strong></h5><ul><li>Th, 12.2.2026 19:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5814">Registration</a></li></ul><p>Explore analytical workflows for peptide therapeutics, including method development, peptide mapping, GLP-1 QC, and LC-MS strategies across Agilent platforms.</p><h5><strong>10. Agilent Technologies: Moving from R&amp;D and Limited QC on a UV-Vis-NIR Instrument to Large-Scale QC Using an Autosampler</strong></h5><ul><li>Th, 12.2.2026 20:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/2104">Registration</a></li></ul><p>This webinar covers practical aspects of adding and using an autosampler to maximize UV-Vis-NIR QC workflows at scale.</p><h5><strong>11. Agilent Technologies: LC Method Transfer – Hidden Challenges &amp; Absolute Solution</strong></h5><ul><li>Fr, 13.2.2026 06:30 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5787">Registration</a></li></ul><p>Discover why LC method transfer between legacy and modern systems is challenging, which hidden parameters affect retention and peak shape, and how to achieve robust, reliable results.</p>

Webinars LabRulezLCMS Week 07/2026

<p><strong>Charge detection mass spectrometry (CDMS) allows direct mass determination of individual ions and is increasingly used to study heterogeneous biological samples. This work demonstrates the use of Orbitrap-based CDMS/Direct Mass Technology (DMT) for quantitative analysis of transthyretin (TTR) tetramer samples below 100 kDa, extending CDMS beyond its traditional qualitative role.</strong></p><p>DMT resolved wild-type and C-terminally modified TTR homotetramers, as well as hybrid tetramers, enabling kinetic analysis of subunit exchange and stability. The approach also quantified thyroxine binding to TTR variants, revealing differences in binding affinity linked to C-terminal modification. By separating overlapping m/z signals through charge measurement, CDMS enables accurate mass and abundance determination, highlighting its potential for quantitative analysis of complex protein systems.</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.analchem.5c05771"><strong>Dissecting Heterogeneous Populations of Protein-Complex Samples Using Direct Mass Technology</strong></a></h4><p>Robert L. Rider, Jared Hampton, Zhenyu Xi, Carter Lantz, Sangho D. Yun, Weijing Liu, Rosa Viner, Arthur Laganowsky, and David H. Russell*</p><p>Anal. Chem. 2025, 97, 49, 27057–27063</p><p><a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1021/acs.analchem.5c05771">https://doi.org/10.1021/acs.analchem.5c05771</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><p>Transthyretin (TTR) is a homotetrameric transport protein that circulates in plasma and cerebrospinal fluid, delivering thyroxine (T<sub>4</sub>) and retinol-binding protein–vitamin A complexes. <a href="javascript:void(0);">(1)</a> The stability of the TTR tetramer is central to its physiological role because dissociation into monomers can initiate misfolding and amyloid formation, leading to systemic or hereditary transthyretin amyloidosis. <a href="javascript:void(0);">(2)</a> Subunit exchange between wild-type (WT) and variant TTR proteoforms, including disease-associated mutations such as V30M and V122I, have been implicated in amyloid progression by generating hybrid tetramers (tetramers containing WT and mutant subunits) with altered stabilities. <a href="javascript:void(0);">(3,4)</a> Ligand binding, particularly at the two thyroxine-binding sites located at the dimer–dimer interface, can kinetically stabilize the tetramer and modulate amyloidogenicity. <a href="javascript:void(0);">(5,6)</a> Accurate measurement of both subunit exchange kinetics and ligand binding stoichiometry is therefore critical for elucidating the TTR dynamics and stability.</p><p>Affinity or sequence tags are widely employed in protein expression, purification, or detection. <a href="javascript:void(0);">(7,8)</a> While these tags are often assumed to be inert, their influence on protein structure and dynamics are rarely examined in detail. <a href="javascript:void(0);">(9,10)</a> Protein tags at the N- and C-terminus of TTR have been shown to have differing gas phase stabilities from those of WT-TTR. <a href="javascript:void(0);">(11)</a> The C-terminus is of particular interest because this region participates in the dimer–dimer interface that governs tetramer stability. <a href="javascript:void(0);">(11,12)</a> Characterizing how the C-terminal tag (CT) (-ASGENLFYQ) affects TTR’s solution stability and ligand binding is not only relevant for understanding TTR dynamics but also provides an example of how expression tags can alter protein dynamics. <a href="javascript:void(0);">(13)</a></p><p>Native mass spectrometry (nMS) has been invaluable for characterizing protein complexes, <a href="javascript:void(0);">(14)</a> yet conventional nMS often struggles with heterogeneous samples where overlapping charge state distributions and adduct heterogeneity limit resolution and quantitation. <a href="javascript:void(0);">(15)</a> Charge detection mass spectrometry (CDMS) addresses these limitations by independently measuring the charge and <i>m</i>/<i>z</i> of individual ions, enabling the direct determination of molecular mass and abundance. Development of CDMS has largely focused on achieving higher mass resolution <a href="javascript:void(0);">(16)</a> and extending measurements toward assemblies into the GDa range. <a href="javascript:void(0);">(17,18)</a> However, there is untapped utility for CDMS experiments other than mass and proteoform determination. Jordan et al. showed the capability to assess conformational heterogeneity of mAb aggregates using the added charge dimension that CDMS provides. <a href="javascript:void(0);">(19)</a> The current work demonstrates that CDMS can separate proteoforms with overlapping <i>m</i>/<i>z</i> values based on charge and quantify their relative abundances in complex mixtures. While nMS is already a highly quantitative technique, our results establish CDMS as an equally powerful tool for quantitative analysis in heterogeneous systems. <a href="javascript:void(0);">(20,21)</a></p><p>Here, we apply Orbitrap-based CDMS/Direct Mass Technology (DMT) using the selective temporal overview of resonant ions (STORI) approach <a href="javascript:void(0);">(22,23)</a> to quantitatively compare WT-TTR and CT-TTR, focusing on two biologically relevant properties: tetramer stability assessed via subunit exchange kinetics and ligand-binding affinity. Conventional nMS cannot fully resolve the overlapping charge states of WT- and CT-TTR or their ligand-bound states. However, DMT can resolve these species by directly measuring the mass (<i>m</i>/<i>z</i> × charge), enabling quantitation of all proteoforms. The data reveal that the CT tag alters tetramer stability and thyroxine-binding affinity, demonstrating the structural sensitivity of TTR to modifications at its C-terminus. More broadly, this work demonstrates the impact that protein tags can have on native protein interactions and highlights the broader utility of quantitative CDMS for probing heterogeneous biological samples.</p><h4><strong>Experimental Section</strong></h4><h5><strong>Data Collection</strong></h5><p>All experiments were conducted on a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/560"><strong>Thermo Scientific Q-Exactive UHMR</strong></a> with added DMT capabilities (Bremen, Germany). Before DMT, mass spectra were collected at various resolving powers (6–200k) for each sample, with the instrument parameters reported in the Supporting Information (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.5c05771/suppl_file/ac5c05771_si_001.pdf">Table S1</a>). For DMT experiments, the trapping gas pressure in the HCD cell was reduced to 0.3–0.8 to attenuate the signal intensity to a single ion level, as well as decreasing the UHV pressure to assist ion retention through the entire transient of Orbitrap analysis. We observed no significant difference between mass spectra collected at various HCD cell pressures (Supporting Information, <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.5c05771/suppl_file/ac5c05771_si_001.pdf">Figure S1</a>). For DMT collection, automated ion control (AIC) and 100% target density were used with 200k resolving power.</p><h4><strong>Results and Discussion</strong></h4><p>CDMS has emerged as a powerful tool for analyzing heterogeneous biomolecular samples, enabling accurate, direct mass determination by simultaneously measuring the charge and <i>m</i>/<i>z</i> for individual ions. While CDMS has been widely applied for qualitative analyses, its potential for quantitative and less than MDa applications remains underexplored. <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05771#fig1">Figure 1</a>A shows the theoretical mass spectrum of WT-TTR (14+ to 16+) and CT-TTR (15+ to 17+) homotetramers, where the two proteoforms become increasingly resolved as the charge states increase (&lt;3900 <i>m</i>/<i>z</i>). <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05771#fig1">Figure 1</a>B zooms in on the 14+ (WT) and 15+ (CT) charge states, highlighting their strong overlap, which prevents accurate deconvolution of the proteoforms by conventional methods. <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05771#fig1">Figure 1</a>C displays theoretical distributions for 0, 1, and 2 T<sub>4</sub> bound states of both WT- and CT-TTR tetramers, where &lt;3900 <i>m</i>/<i>z</i> has observable separation between all proteoforms. However, for the 14+ and 15+ charge states of WT- and CT-TTR, respectively, the 0 T<sub>4</sub>- and 1 T<sub>4</sub>-bound populations overlap (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05771#fig1">Figure 1</a>D). Furthermore, commonly adducted species (Na<sup>+</sup>, K<sup>+</sup>, and Zn<sup>2+</sup>) observed in experimental spectra broaden these distributions, making it increasingly difficult to distinguish and deconvolute the proteoforms (see <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.5c05771/suppl_file/ac5c05771_si_001.pdf">Figure S2</a>). Here, we employ Orbitrap-based CDMS/DMT to overcome this <i>m</i>/<i>z</i> overlap to resolve and quantify hybrid tetramer formation and T<sub>4</sub> binding.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Anal_Chem_2025_97_49_27057_27063_Figure_1_A_Theoretical_mass_spectra_of_WT_TTR_and_CT_TTR_homotetramers_47232849d9.jpg" alt="Anal. Chem. 2025, 97, 49, 27057–27063: Figure 1. (A) Theoretical mass spectra of WT-TTR and CT-TTR homotetramers. (B) Zoomed-in view of the 14+ WT-TTR and 15+ CT-TTR distributions to show the large overlap of the proteoforms. (C) Theoretical mass spectra of WT-TTR and CT-TTR homotetramers with thyroxine (T4) binding. (D) Zoomed-in view of the 14+ WT-TTR and 15+ CT-TTR distributions where the 0 and 1 T4 have overlapping distributions. These theoretical distributions do not contain any commonly adducted species (Na+, K+, Zn2+), which broaden the distributions and create more overlap even for the proteoforms in the range 3300–3900 m/z (see Figure S2)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Anal_Chem_2025_97_49_27057_27063_Figure_1_A_Theoretical_mass_spectra_of_WT_TTR_and_CT_TTR_homotetramers_47232849d9.jpg 187w," sizes="100vw" width="1417" height="1182"></p><h5><strong>Thyroxine Binding to TTR Homotetramers</strong></h5><p>Thyroxine is the less active form of a thyroid hormone important for metabolism that binds to TTR for transport throughout plasma and cerebral spinal fluid. <a href="javascript:void(0);">(31)</a> Turnover of T<sub>4</sub> into T<sub>3</sub> (active) occurs after dissociation, where it can then modulate gene expression via binding to nuclear receptors. <a href="javascript:void(0);">(32)</a> The TTR tetramer gains substantial stability as it binds up to 2 T<sub>4</sub> at the tetramer interface, decreasing tetramer dissociation and SUE. <a href="javascript:void(0);">(33)</a> This has been shown previously to decrease the amyloidogenic rate of TTR, which led to tafamidis (similar in structure to T<sub>4</sub>) to be designed and is currently the only drug that is approved for clinical treatment of TTR amyloidosis. <a href="javascript:void(0);">(34)</a> Measuring the difference in binding affinity between TTR proteoforms may provide insight into regions of TTR or TTR intermolecular/intramolecular interactions that are important for binding of small molecules such as tafamidis and T<sub>4</sub>.</p><p>DMT was further applied to quantify T<sub>4</sub> binding to WT- and CT-TTR homotetramers, highlighting the technique’s utility in probing protein–ligand interactions. <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05771#fig3">Figure 3</a>A shows a representative mass spectrum of TTR homotetramers in the presence of T<sub>4</sub>. While ligand-bound species can be observed, homotetramers cannot be confidently resolved across the entire 3000–5000 <i>m</i>/<i>z</i> range. By leveraging the charge-resolving capabilities of DMT, we achieve separation of the homotetramers (<a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05771#fig3">Figure 3</a>B,C) and the 0, 1, and 2 ligand-bound states. The 2D plot clearly shows the gain in resolution achieved when charge is simultaneously measured with <i>m</i>/<i>z</i> by separating the 14+ and 15+ charge states for WT and CT, respectively, in the range 3900–4200 <i>m</i>/<i>z</i>. Additionally, using ion mobility does not provide the same kind of 2D resolution due to the similarity in arrival times for the homotetramer proteoforms, as evidenced by <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.5c05771/suppl_file/ac5c05771_si_001.pdf">Figures S4 and S5</a> (see the Supporting Information). These data provide evidence that when ion mobility is able to separate out species that overlap in <i>m</i>/<i>z</i> yet differ in mobility, CDMS could be an alternative or used complementarily since the species likely also differ in charge.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Anal_Chem_2025_97_49_27057_27063_Figure_3_A_Mass_spectra_of_WT_TTR_and_CT_TTR_homotetramers_with_thyroxine_binding_61b1e98a94.jpg" alt="Anal. Chem. 2025, 97, 49, 27057–27063: Figure 3. (A) Mass spectra of WT-TTR and CT-TTR homotetramers with thyroxine binding. Ligand binding can be resolved, but homotetramers cannot be confidently identified. Charge states labeled are for WT; CT is always one charge state higher at the same m/z range. (B) DMT heatmap resolving WT-TTR and CT-TTR homotetramers with the additional measurement of charge. (C) Deconvoluted mass spectrum from DMT analysis. Both homotetramers and their ligand binding are resolved, and fit for analysis is shown in red. (D) Mole fraction of each homotetramer and their thyroxine binding species. Error bars represent the standard deviation of replicates (n = 3). The significance for each ligand state is in respect to the left adjacent state. *p &lt; 0.05." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Anal_Chem_2025_97_49_27057_27063_Figure_3_A_Mass_spectra_of_WT_TTR_and_CT_TTR_homotetramers_with_thyroxine_binding_61b1e98a94.jpg 181w," sizes="100vw" width="1266" height="1094"></p><h4><strong>Conclusion</strong></h4><p>This work demonstrates that quantitatively, Orbitrap-based CDMS/DMT can determine differences in protein-complex stability and ligand binding. By directly comparing WT- with CT-TTR, we show that the CT tag accelerates tetramer dissociation while enhancing T<sub>4</sub> binding affinity. These results indicate that the C-terminus, located at the dimer–dimer interface, plays a more significant role in TTR stability and ligand recognition than previously appreciated. <a href="javascript:void(0);">(12)</a> Even the addition of a short peptide sequence perturbs noncovalent interactions at the interface, likely altering solvent accessibility, and the dynamics of the thyroxine binding channel. <a href="javascript:void(0);">(37,54)</a> Such findings underscore the importance of evaluating how seemingly minor sequence modifications, such as affinity tags, can influence fundamental biophysical properties.</p><p>Beyond TTR, this work positions quantitative CDMS as a broadly applicable strategy for analyzing heterogeneous protein systems, where charge domain separation overcomes the resolution limits of <i>m</i>/<i>z</i> domain measurements in traditional nMS experiments. While much of the field has emphasized extending CDMS to ultrahigh masses and maximal resolution, <a href="javascript:void(0);">(16,18)</a> our results highlight the underexplored potential of applying the method in the 1000–10,000 <i>m</i>/<i>z</i> range common to nMS experiments. This capability is directly relevant to heterogeneous membrane protein complexes, which often display broad distributions of oligomeric states, PTMs, lipid, and ligand adducts that complicate spectra. <a href="javascript:void(0);">(48,55)</a> Similarly, mAbs can oligomerize and exhibit mass heterogeneity from variable glycosylation, affecting pharmacokinetics, effector function, and stability. <a href="javascript:void(0);">(19)</a> CDMS may resolve and quantify such proteoforms in a single experiment without the need for charge reduction or chemical derivatization. <a href="javascript:void(0);">(48,56,57)</a></p>

Dissecting Heterogeneous Populations of Protein-Complex Samples Using Direct Mass Technology

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Organomation, founded in 1959, designs and manufactures high-quality nitrogen evaporators and extraction systems. Known for innovation and durability, their lab instruments are used globally for efficient sample preparation with strong customer support.

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Thermo Scientific AcquireX Intelligent Data Acquisition Workflow

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

Thermo Scientific mzCloud Mass Spectral Library

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

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

Thermo Scientific Proteome Discoverer Software

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

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

Thermo Scientific™ SimGlycan™ Software

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

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

Thermo Scientific LC-MS Data Processing Software

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

Thermo Scientific Ardia Platform

Built using cloud technology, the Ardia Platform centralizes information, including scientific data and results, maximizes instrument utilization, and accelerates data analysis to help scientists get closer to the truth.

<h3><strong>Bring your laboratory into a new era of connectivity with the Ardia Platform</strong></h3><p data-start="64" data-end="714"><strong>Digital transformation is a journey driven by the desire to fundamentally improve laboratory working practices by leveraging the latest advances in IT. The Thermo Scientific™ Ardia™ Platform allows the laboratory to harness the same technology.&nbsp;</strong></p><p data-start="64" data-end="714">In an era where laboratories are uncompromising in their pursuit of efficiency, the demand for software that seamlessly connects data, instruments, and scientists is on the rise.</p><p data-start="64" data-end="714">Built using cloud technology, the Ardia Platform centralizes information, including scientific data and results, maximizes instrument utilization, and accelerates data analysis to help scientists get closer to the truth.</p><figure class="image"><img style="aspect-ratio:1440/1127;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_2_4c83f21ef8.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_2_4c83f21ef8.jpg 200w," sizes="100vw" width="1440" height="1127"></figure><h5><strong>Centralize</strong></h5><p>Revolutionize data management by bringing together all your data sources, formats, and applications into one platform. With centralized data, you gain unprecedented control, accessibility, and efficiency, enabling you to make data‑driven decisions with confidence.</p><h5><strong>Unify</strong></h5><p>Say goodbye to the complexities of managing data scattered across various systems and locations. The Ardia Platform integrates with a growing list of software tools and applications for direct data access and automated data transfer, allowing you to harness the power of a unified platform and help eliminate data silos.</p><h5><strong>Streamline</strong></h5><p>Eliminate time‑consuming manual data transfers with automated workflows via the Ardia Platform’s Data Sync tool. Automatically transfer data to and from your repository for applications that are not yet connected so users can focus on what matters most.</p><h5><strong>Collaborate</strong></h5><p>Collaboration goes beyond just centralizing data and integrating software. With a single platform, you can easily share, access, and collaborate on data. Real‑time data updates, shared dashboards, and collaborative tools facilitate efficient teamwork, accelerating project timelines and driving innovation</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_57590fecf7.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_57590fecf7.jpg 245w," sizes="100vw" width="1022" height="450"></p><h3><strong>Data management</strong></h3><p>Securing, managing, and effectively utilizing large volumes of scientific data stored across multiple devices in different formats can be challenging and time-consuming.<br>The Ardia Platform offers robust data management capabilities that address these challenges. With automated central data storage, including backup and archival capabilities, and comprehensive access controls, users can securely access, view, and organize information from various applications more effectively.</p><blockquote><p><strong>webinar: </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/4962"><strong>Take control of your data and instruments</strong></a></p></blockquote><div><div data-message-author-role="assistant" data-message-id="ba34c04b-e6ae-4d15-ac9e-9e3606bb4933" dir="auto" data-message-model-slug="gpt-4o"><div><div><h4><strong>Centralize your data and enable accessibility and security</strong></h4><h5><strong>Manage</strong></h5><p data-start="64" data-end="990">The Ardia Platform provides secure, single‑point data management with automated transfer of data and results from <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong>Thermo Scientific™ Chromeleon™ Chromatography Data System</strong></a><strong>, </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1758"><strong>Xcalibur™</strong></a><strong>,</strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong> Compound Discoverer™</strong></a><strong>, </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1782"><strong>Proteome Discoverer™</strong></a><strong>,</strong> and<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1837"><strong>BioPharma Finder™ software</strong></a>, as well as third‑party application data via the Ardia Platform’s Data Sync functionality.<br>With single‑point data storage, users can enhance data accessibility, improve data organization and discovery, and reduce or eliminate data duplication.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_3_0ea16b74db.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_3_0ea16b74db.jpg 245w," sizes="100vw" width="1440" height="544"></p><h5><strong>Secure</strong></h5><p data-start="64" data-end="990">Keep data secure and controlled with user login access, system‑generated audit trails, and embedded user and data management tools, customizable to your organization’s specific needs. Streamline your operations and ensure disaster resilience through built‑in capabilities, such as tracking actions and simplifying data backup and archiving.</p></div></div></div></div><h3><strong>Ardia Platform’s Data Viewer</strong></h3><p>The intuitive, web‑based Ardia Platform’s Data Viewer tool provides a <strong>single location</strong> for review of chromatography and mass spectrometry data, delivering consistency across software products integrated with the Ardia Platform.<br>With a new user interface, it’s easy to display chromatograms and spectra, quickly create extracted ion chromatograms, perform peak integration, export spectral data to the<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud™</strong></a> library for easy compound annotation, and view diagnostic channels like pump pressure for troubleshooting.<br>Expedite data review with user‑friendly features that include the ability to import a mass list, export plots in .svg format for high‑resolution visualizations, and quickly display linked data‑dependent acquisitions.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_4_9d3c486827.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_4_9d3c486827.jpg 245w," sizes="100vw" width="1918" height="1012"></p><h3><strong>Instrument management</strong></h3><p>Managing a set of individual instruments is often a manual, time-consuming task. Bringing them together in one place, the Ardia Platform’s Instrument application enables monitoring and management of all connected instruments to maximize utilization and eliminate paper records.<br>This can significantly improve productivity by minimizing downtime, reducing delays, and improving lab efficiency.</p><h4><strong>Effective instrument management to drive laboratory productivity</strong></h4><h5><strong>Monitor</strong></h5><p>Easily view all connected systems from a central location with instrument cards providing real‑time status and data acquisition information for a holistic laboratory view to enable fast, informed decisions.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_5_f985768d28.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_5_f985768d28.jpg 245w," sizes="100vw" width="1692" height="809"></p><h5><strong>Record</strong></h5><p>Digitize, standardize, and centralize instrument logbooks with automated event logging, plus manual entry tools to record maintenance activities, custom notes, and images. Automatic tracking of instrument module movements between systems assists laboratories in maintaining accurate and complete records, helping to ensure instruments are controlled and working properly, instilling confidence in result reliability. Instrument support is accelerated via in‑app service ticket and support package generation for immediate delivery to Thermo Fisher Scientific technical support.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_6_1a2b159f68.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_6_1a2b159f68.jpg 200w," sizes="100vw" width="873" height="680"></p><h5><strong>Schedule</strong></h5><p>Increase laboratory efficiency by optimizing instrument utilization. The Ardia Platform’s Instruments Scheduler tool provides a single point to plan work, view system availability, reserve time, and set maintenance windows on all connected instruments to minimize downtime.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_7_01ca77bc6d.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_7_01ca77bc6d.jpg 245w," sizes="100vw" width="1483" height="548"></p><h5><strong>Utilize</strong></h5><p>The Ardia Platform’s Data Insights application provides out‑of‑the‑box dashboards for key laboratory insights on resource availability, instrument status, and instrument performance in a centralized location. Track and monitor system metrics such as injection quantity, time, volume, type or status, and % utilization across systems and geographical locations. With interactive dashboards that can be filtered by system, system type, location, project, or time, you can easily focus on the metrics that matter most.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Ardia_Platform_8_3a6b276497.jpg" alt="Thermo Scientific Ardia Platform." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Ardia_Platform_8_3a6b276497.jpg 245w," sizes="100vw" width="1920" height="937"></p>

Thermo Scientific™ BioPharma Finder™ Software for the Characterization of Biotherapeutics

Simplify comprehensive biotherapeutic attribute characterization with advanced capabilities to increase throughput and confidence in a connected environment.

<div><div container-id="cq-colctrl-lt7" comp-id="A1"><div><p><strong>Discover how the features of Thermo Scientific BioPharma Finder Software are engineered to support the world of complex biopharmaceutical characterization. Featuring novel data processing algorithms and easy-to-interpret data visualization tools, the software supports users looking to confidently characterize biopharmaceuticals.</strong></p><p>Power BioPharma Finder&nbsp;Software with the<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1821"> <strong>Thermo Scientific Ardia Platform</strong></a> to automate file centralization during acquisition, expand file access, enable report creation and result sharing, and remove data management barriers from your daily routine.</p><div><h3><strong>Key benefits</strong></h3></div><div><ul><li><strong>Confident characterization: </strong>Explore a solution for confident animo acid sequence characterization with the <strong>Peptide Mapping Analysis</strong> module featuring a novel MS<sup>2</sup> prediction algorithm.</li><li><strong>Customized Nucleotide sequence support:</strong> Leverage the ability to create customized nucleotide sequences to support confirmation with the <strong>Oligonucleotide Analysis </strong>module featuring an improved MS<sup>2</sup> fragmentation model (available in BioPharma Finder Software version 5.3).</li><li><strong>Efficient data handling:</strong> Move through vast amounts of data with remarkable efficiency using the <strong>Intact Mass Analysis</strong> module. With innovative deconvolution algorithms and features, you can generate multi-consensus reports effortlessly, providing a comprehensive view of your results.</li><li><strong>Unparalleled Modification Exploration and Flexibility: </strong>The <strong>Top-Down Analysis</strong> module empowers you to search through an extensive range of modifications, even at the per-peak level. With multiple fragmentation modes and a cross-array processing algorithm, you have the flexibility to explore your samples in greater detail.</li><li><strong>Seamless integration: </strong>See how easy it is to move from sophisticated characterization using BioPharma Finder Software to confident quantitation in <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong>Chromeleon CDS software</strong></a> with benefits added by the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1821"><strong>Ardia Platform</strong></a> including connecting instrument data, supporting global access and centralizing BioPharma Finder reports.</li></ul><h3><strong>Learn more about BioPharma Finder Software</strong></h3><div><p>The<strong> right combination </strong>of data and software makes all the difference in accurately characterizing molecules, especially for large molecule.</p><h4><strong>Peptide mapping analysis</strong></h4><p>Characterization of a macromolecule comprised of an amino acid sequence can involve a lot of moving targets. Techniques for confident confirmation typically include comparisons of data collected against theoretical knowledge of the sequence. The best processing tools will also give users the ability to model probable sequences against the data collected with easy-to-use tools to increase the confidence of the identification and supply the summary reports with easy-to-interpret results.</p><div><h5><strong>Featured in the Peptide Mapping Analysis</strong></h5><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_b88e243207.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software: Processing with the novel MS2 algorithm in the Peptide Mapping Analysis module, generates a predictive model that includes Kinetical predictions that are compared with the measured spectra to increase confidence in the identification." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_b88e243207.jpg 245w," sizes="100vw" width="1160" height="540"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_2_6dda72b394.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  These processing tools, when combined, produce intuitive result review tools including comprehensive coverage maps, deep dive spectral comparison views and graphical sample comparison options." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_2_6dda72b394.jpg 245w," sizes="100vw" width="1160" height="600"></p><div><h5><strong>Detect and quantify host cell proteins</strong></h5></div><div><p>The sensitivity of the detection algorithm and prediction analytics allow for high confidence even for low abundance targets to support residuals applications like Host Cell Protein (HCP) analysis.</p></div><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_3_e493898dc1.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software: Detect and quantify host cell proteins." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_3_e493898dc1.jpg 245w," sizes="100vw" width="1160" height="600"></p></div><h4><strong>Oligonucleotide analysis</strong></h4><div><p><strong>Sequence confirmation </strong>for oligonucleotides can be daunting. Take the question out of sequence confirmation with our enhanced MS<sup>2</sup> predictive algorithms that can iteratively create the best array of possibilities without iterating into infinity. Summarize your characterization with visual tools, generate easy-to-interpret results and enhance collaboration by saving and sharing reports in a connected environment.&nbsp;&nbsp;</p><h5><strong>Featured in the Oligonucleotide Analysis module</strong></h5><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_4_f709ce5528.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  The oligonucleotide sequence editor provides an easy-to-use interface for quickly and easily building and visualizing customized oligonucleotide sequences. Build out multiple expected sequences from custom building block subunits, a wide selection of modifications from the predefined list or with user-defined custom modifications." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_4_f709ce5528.jpg 245w," sizes="100vw" width="1160" height="600"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_5_f204e2cd40.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  Eliminate alternative possibilities based on the entered sequence with the random sequence generator and leverage the in silico digest tools to support confident sequence verification - all using an updated MS2 prediction algorithm (available in BioPharma Finder Software version 5.3)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_5_f204e2cd40.jpg 245w," sizes="100vw" width="1160" height="600"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_6_f7f2d9e029.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  Perform mRNA mapping with selected in silico mRNA digestion or define the cleavage locations manually. Dig into the identity of fragments and expected or unexpected modifications and assess the overall coverage with intuitive visual coverage maps." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_6_f7f2d9e029.jpg 245w," sizes="100vw" width="1160" height="600"></p></div><h4><strong>Intact mass analysis</strong></h4><div><div container-id="cq-colctrl-lt2" comp-id="B1"><div><p>Intact analysis on its face is a simple mathematical calculation used to deconvolute a series of m/z values into components but throw in the complexity of large molecule targets with modifications in a mixture of other like-molecules and mass accuracy becomes harder to achieve. No matter your data resolution,<strong> leverage innovative software tools engineered</strong> to filter and process through complex spectra with the <strong>Intact Analysis module.</strong> Discover how to quickly acquire and process batches of samples supported by a central data location on the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1821"><strong>Ardia Platform</strong></a> and speed through large batch-to-batch comparison studies to create summaries with connected multi-consensus reports.</p><div><h5><strong>Featured in the Intact Analysis module</strong></h5><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_7_72cfbd44c3.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  Accurately determine molecular weights utilizing the Sliding Window algorithm coupled with our optimized Xtract (for high resolution) and Respect (for lower resolution) deconvolution algorithms. Achieve comprehensive detection, even for co-eluting, low-intensity components in complex mixtures and account for any shifts in retention time." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_7_72cfbd44c3.jpg 245w," sizes="100vw" width="1160" height="323"></p></div><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_8_d0c92fbca9.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  Use the expanded sequence matching capabilities for oligonucleotides which includes the ability to perform Terminal Truncation Searching from either the 3' or 5' terminus, facilitating the identification of impurities with greater ease. " srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_8_d0c92fbca9.jpg 245w," sizes="100vw" width="1160" height="600"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_9_d345484402.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  The intact mass analysis of heavily modified oligonucleotides presents analytical and data processing challenges due to the frequent usage of sulfur modifications. Pairing Thermo Scientific Orbitrap mass spectrometers with BioPharma Finder Software allows for confident intact mass identification of phosphorothioate conversion of oligonucleotides with less than 5 ppm error." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_9_d345484402.jpg 245w," sizes="100vw" width="1160" height="600"></p></div></div></div><h4><strong>Top-down analysis</strong></h4><div><div container-id="cq-colctrl-lt2" comp-id="B1"><div><p><strong>Higher order structure characterization</strong> requires a combination of some of the most variable sample treatment techniques, variable data acquisition techniques, and combined or complex data processing techniques. Looking to gently pry apart large complexes without reducing them to their smallest parts and understand them is an art and a science that can be supported by the <strong>Top-Down Analysis module</strong>. Explore the tools offered to help refine the field of predicted possibilities without restricting them, the support for multi fragmentation mode data, and the easy-to-use multi-consensus summaries to understand your molecule.</p><div><h5><strong>Featured in the Top-Down Analysis module</strong></h5><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_10_7e7ef85413.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  With the ProSightBP processing tool users can set variable or static sites for modification, select peak specific deconvolution parameters and even select peak specific sequence searching then let ProSightBP create the predictions. Combine the data from multi fragmentation modes including CID, HCD, ETD, EThcD, and UVPD resulting in confident identification." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_10_7e7ef85413.jpg 245w," sizes="100vw" width="1160" height="600"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_11_e3c9f5084b.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  Combining the predictive power of ProSight BP against the deconvoluted accurate mass with the sequence coverage from ETD and UVPD fragmentation reveals a comprehensive set of results to support confident molecule characterization." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_11_e3c9f5084b.jpg 245w," sizes="100vw" width="1160" height="600"></p></div></div></div></div><h4><strong>Connecting to the Ardia Platform</strong></h4><div><p>Living in a world connected by networks that enable people to share everything doesn’t have to stop in the lab. With the<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1821"><strong> Ardia Platform</strong></a> see how easy it can be to automatically centralize files, connect into those files from anywhere and process them with <strong>BioPharma Finder Software</strong> or any connected application.&nbsp;&nbsp;</p><div><h5><strong>Featured enhancements through connection</strong></h5><div><div container-id="cq-colctrl-lt2" comp-id="B1"><div><p><strong>Faster data review</strong></p><ul><li>Review a result generated by<strong> another colleague</strong> without having to import the results, open it from the shared secured Ardia Platform data repository, make comments or changes, and the software will automatically generate a new version to record the changes.</li></ul><p><strong>Better data management with centralized secured data</strong></p><ul><li>All results are <strong>securely </strong>saved in one place, no more finding the “right” computer or hard drive that contains the experiment and data.</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_12_b6a814cd90.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  Keep data secure and controlled. Gain insights into file history, method history, and manage user access with control." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_12_b6a814cd90.jpg 245w," sizes="100vw" width="1160" height="600"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Bio_Pharma_Finder_Software_13_1e3b879f18.jpg" alt="Thermo Scientific™ BioPharma Finder™ Software:  Save and review individual reports without having to open BioPharma Finder Software for oligonucleotide, peptide mapping and intact mass applications. Utilize default reporting templates to speed development of customized reports and effectively modify templates to achieve desired result summary with the help of the customizable report designer." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Bio_Pharma_Finder_Software_13_1e3b879f18.jpg 245w," sizes="100vw" width="1160" height="600"></p><p>Enable collaboration on a global scale in a secure fashion to collaborate, compare, track, and finalize peptide results and workbooks using dynamic versioning history. Accelerate method optimization and review through a shared secure environment.</p></div></div></div></div></div></div></div></div></div></div>

Thermo Scientific™ Chromeleon™ XPS Open Access Software

Thermo Scientific™ Chromeleon™ XPS provides streamlined and easy-to-use interface for Thermo Scientific™ Chromeleon™ CDS, while maintaining full capabilities of the CDS software.

<p><strong>In modern laboratories, chromatography techniques and the use of mass spectrometry (MS) detection are in high demand. Until recently, MS detectors were regarded as sophisticated detection tools that could be operated only by a highly trained specialist. Nowadays mass spectrometers are increasingly used as straightforward detectors for chromatography.</strong></p><p>Alongside this move into routine use of MS is the continued deskilling of staff in the laboratory world, causing highly experienced chromatographers to be in short supply. The result is a substantial number of regular scientists and process operators that need to generate chromatographic results using advanced instrumentation themselves.</p><p>The solution is an Open Access tool enabling users to simply walk up and use a very straightforward interface to exploit the full power of the chromatography data system (CDS), without actually using the CDS software itself. <strong>Thermo Scientific™ Chromeleon™ XPS </strong>provides this <strong>streamlined and easy-to-use</strong> interface for <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong>Thermo Scientific™ Chromeleon™ CDS</strong></a>, while maintaining <strong>full capabilities</strong> of the CDS software, like instrument control, data processing, reporting and compliance tools.</p><h3><strong>Workflow</strong></h3><p>Users can walk up to <strong>any chromatography instrument</strong> connected to the CDS, with or without MS detection, and start to run their analysis with only a <strong>few mouse-clicks.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_5e8f8c3dec.jpg" alt="Thermo Scientific™ Chromeleon™ XPS Open Access Software: First, select the analysis to perform (A) and which instrument should be used (B). The instrument overview shows the current instrument status’ and displays the estimated wait time until each instrument is available and the number of sample positions still available.  The instrument list is filtered depending on the analysis selected and the users privileges to only show appropriate instruments." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_5e8f8c3dec.jpg 196w," sizes="100vw" width="876" height="697"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_2_a8b64a52ae.jpg" alt="Thermo Scientific™ Chromeleon™ XPS Open Access Software: Next, enter the sample names (C) and any other parameters (D) required for the analysis." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_2_a8b64a52ae.jpg 196w," sizes="100vw" width="876" height="697"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_3_4b4367ffae.jpg" alt="Thermo Scientific™ Chromeleon™ XPS Open Access Software: Place the sample vials in the indicated positions and select Submit." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_3_4b4367ffae.jpg 196w," sizes="100vw" width="876" height="697"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_4_0386d31c9a.jpg" alt="Thermo Scientific™ Chromeleon™ XPS Open Access Software: The sequence is submitted and will run. The operator is shown the expected start and finish time of the analyses." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_4_0386d31c9a.jpg 245w," sizes="100vw" width="625" height="263"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_5_1b51ab8dd2.jpg" alt="Thermo Scientific™ Chromeleon™ XPS Open Access Software: At the end of the run, the results are automatically printed and/or exported and a link to the exported report can be distributed via email." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_5_1b51ab8dd2.jpg 245w," sizes="100vw" width="814" height="309"></p><h3><strong>Configuration and management</strong></h3><p>Running samples is as easy as described above once Chromeleon XPS software is set up, configured and managed by an experienced chromatographer.</p><ul><li>All the methods required for the analysis must be created; the instrument method with all instrument control and data acquisition parameters, the processing method with all data processing parameters and the report template with all required results, to be reported.&nbsp;</li><li>A Chromeleon eWorkflow is created using these methods. An eWorkflow is an electronic procedure that automates all steps of the laboratory process related to a chromatographic analysis</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_6_a3b2219e42.jpg" alt="Thermo Scientific™ Chromeleon™ XPS Open Access Software: The lab manager can customize Chromeleon XPS to show or hide individual toolbar buttons (A), which eWorkflows are visible to users (B) and which instruments they can access (C)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_6_a3b2219e42.jpg 196w," sizes="100vw" width="876" height="697"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_7_d647111f5d.jpg" alt="Thermo Scientific™ Chromeleon™ XPS Open Access Software: In addition, it is possible to define various system options, such as which email notifications to send." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_Chromeleon_XPS_Open_Access_Software_7_d647111f5d.jpg 193w," sizes="100vw" width="659" height="533"></p><p>Chromeleon XPS Open Access software lets <strong>any user</strong> run samples on their own by delivering a <strong>clean, streamlined walk-up interface</strong> that utilizes the<strong> full power</strong> of Chromeleon CDS. Users can access<strong> all instruments controlled by </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong>Chromeleon CDS</strong></a><strong>, including MS</strong>, and automatically receive results or notifications about run completion or failure. The management console contains advanced customization options to fulfill any organization’s requirements, included fully regulated environments.</p><p><strong>Chromeleon XPS software provides error-free execution of any chromatography analysis with minimal training requirements for users.</strong></p>

Thermo Scientific LCQUAN Quantitative Software

LCQUAN is a robust, 21 CFR Part 11-compliant software for LC-MS/MS bioanalysis, providing complete tools for data acquisition, review, and secure management in drug development workflows.

<h4><strong>21 CFR Part 11-compliant software for quantitative LC-MS/MS data acquisition and management</strong></h4><p><strong>Thermo Scientific™ LCQUAN™ quantitative software is a robust, regulatory-compliant data system tailored for bioanalytical laboratories conducting LC-MS/MS assays. Developed in close collaboration with pharmaceutical industry experts, LCQUAN provides all the tools needed to acquire, process, review, and securely manage quantitative data across global drug development workflows.</strong></p><h3><strong>Key Features</strong></h3><h4><strong>Regulatory Compliance</strong></h4><ul><li>Fully compliant with FDA 21 CFR Part 11 requirements for electronic records and signatures</li><li>Enables secure submission of electronic documents to regulatory agencies, including the FDA</li></ul><h4><strong>Comprehensive Workflow</strong></h4><ul><li>Guides users step-by-step through acquisition, method development, data review, processing, reporting, and export</li><li>Supports import of sequence information from external systems</li><li>Streamlines interaction with Thermo Scientific™ Watson LIMS™ for GLP-compliant bioanalytical studies</li></ul><h4><strong>Secure Data Management</strong></h4><ul><li>Enables data processing on networked systems, including secure remote disks</li><li>Centralized, workbook-style data storage for easy archiving and retrieval</li><li>Multi-level user privileges—from full system access to read-only modes</li></ul><h4><strong>Seamless LIMS Integration</strong></h4><ul><li>Bi-directional communication with Watson LIMS facilitates study tracking, chromatogram review, auditing, and compliance</li><li>Optimized for regulated pharmaceutical workflows from discovery through clinical trials</li></ul><h4><strong>Proven Platform</strong></h4><ul><li>Part of an integrated Thermo Scientific LC-MS/MS solution suite, including TSQ Series mass spectrometers and FAIMS interface technology</li><li>Ensures high sensitivity, robustness, and reproducibility for regulated bioanalytical assays</li></ul>

Thermo Scientific™ TraceFinder™ Software

Driven by a powerful and intuitive set of acquisition and data processing tools, Thermo Scientific TraceFinder software provides rapid access to your results and increases output across the entire laboratory.

Products from category GC, LC and MS data processing distributed by Thermo Fisher Scientific (EMEA) - page 1

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