<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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<p><strong>Nitrosamine (genotoxic) impurities have been found in some angiotensin II receptor blocker (ARB) medicines, such as valsartan, and more recently in histamine-2 receptor blocker medicines, such as ranitidine, drawing close scrutiny from FDA, the European Medicines Agency (EMA) and other regulatory bodies leading to product recalls.</strong></p>
<p>Gas chromatography–mass spectrometry (GC-MS) has typically been the detection technique of choice; however, not all nitrosamines can be analyzed this way. As the number of known nitrosamines requiring trace level quantitation increases, the greater the need for robust, sensitive, and high-throughput assays to provide a cost-sensitive approach of a single analysis capable of accurately measuring all compounds. The use of liquid chromatography with high-resolution MS (LC-HRMS) allows low level detection and high confidence of a wider range of nitrosamine impurities.</p>
<h3><strong>Session breakdown:</strong></h3>
<h5>11:00 CEST, 10 minutes + Q &amp; A</h5>
<p><strong>Introduction to impurity analysis challenges and regulatory requirements in Europe</strong></p>
<p><em>Presenter: Jon Bardsley,Pharmaceutical Marketing Manager , Thermo Fisher Scientific</em></p>
<h5>11:20 CEST,  20 minutes + Q &amp; A</h5>
<p><strong>Chromatography and Mass Spectrometry software for GMP impurity testing</strong></p>
<p><em>Presenter: Darren Barrington-Light, Software Product Marketing Manager, Thermo Fisher Scientific</em></p>
<p>This session will give an overview of the current landscape of impurity testing in general and with a focus on nitrosamines and the European regulations.   We will then cover our software, Chromeleon for Mass Spectrometry with an overview and focus on data integrity and compliance. You will have a chance to ask questions to our specialists on these topics.</p>
<h3><strong>Key Learning Objectives:</strong></h3>
<ul>
<li>Why is the analysis of genotoxic impurities important?</li>
<li>Method development considerations for trace level impurities</li>
<li>What are the current regulations in Europe?</li>
<li>The role of compliance in data software with mass spectrometry</li>
</ul>
<blockquote>
<p><strong>Presenter: Darren Barrington-Light (Senior Product Marketing Manager, Enterprise Chromatography Data Systems, Thermo Fisher Scientific)</strong></p>
</blockquote>
<blockquote>
<p>Having worked in Chromatography throughout his careerin the fieldsof analytical chemistry, chromatography hardware and computer software,specifically Chromatography Data Systems,for over25years, Darren has a unique understanding of the requirements of organizations that rely on chromatography data to manage their day to day operations. As capabilities have advanced, Darren has worked with clients across multiple industries to show them how Thermo Scientific Chromeleon CDS software can help them to improve their day to day operations and drive fast, informed decisions.</p>
</blockquote>
<blockquote>
<p><strong>Presenter: Jon Bardsley (Pharma &amp; BioPharma Manager, Thermo Fisher Scientific)</strong></p>
</blockquote>
<blockquote>
<p>Jon Bardsley has over a decade of experience of small-molecule pharmaceutical DMPK and regulated bioanalytical studies within with large Pharmaceutical environments. His passion for development of robust and accurate analytical methods for high-throughput studies has seen him also gain experience in contract research organizations. Jon sits on the ReidBioAnalyticalcommittee of the Chromatography Society and is a subject matter expert in the bioanalysis community. Following a period as Senior Applications Specialist for Chromatography, Jon now holds the position of Vertical Marketing Specialist for Pharma &amp;BioPharmawithin Thermo Fisher Scientific, with a view to bringing relevant technologies together to help solve customer challenges.</p>
</blockquote>


Thermo Fisher Scientific: Virtual seminar session 1: Impurity analysis with a focus on nitrosamines

Virtual seminar session 1: Impurity analysis with a focus on nitrosamines

<p><strong>Proteomics and metabolomics have become widely adopted techniques, often multi-disciplinary, requiring the collaboration of biologists and medical doctors, of protein chemists, mass spectrometrists and bioinformaticians delivering the value of innovative applications and novel workflows as fresh knowledge on health, disease and biology. This field relies on the scientific community pushing the limits of mass spectrometry (MS) technology to gain understanding in various disease areas that can lead to effective diagnostics, treatments and vaccines. Over this day, we will highlight several of these cutting-edge developments and results in single cell analysis, spatial omics and clinical research deploying artificial intelligence for improved data acquisition and interpretation. Our specialists will also share their recommendations for achieving outmost performance with our instruments and software.</strong></p>
<h5><strong>9:00 BST (10:00 CEST - Prague) | Plenary 1 | Your fast-track to confident results in multi-omics: Thermo Scientific Orbitrap Exploris product family expanded</strong></h5>
<ul>
<li><strong>Speaker:</strong> Thomas Moehring, Sr Director Marketing LSMS, Thermo Fisher Scientific</li>
</ul>
<h5><strong>9:30 BST  (10:30 CEST - Prague) | Plenary 2 | Latest developments in native ambient mass spectrometry</strong></h5>
<ul>
<li><strong>Speaker:</strong> Helen Cooper, Professor of Mass Spectrometry, Deputy Head of School, EPSRC Established Career Fellow, Birmingham University</li>
</ul>
<blockquote>
<p><strong>Presenter: Thomas Moehring (Sr Director Marketing LSMS, Thermo Fisher Scientific)</strong></p>
</blockquote>
<blockquote>
<p>Dr. Thomas Moehring studied Chemistry and Environmental Science at the Carl von Ossietzky University Oldenburg, Germany, and completed his Ph.D. project at the Institute of Chemistry and Biology of Marine Environment (ICBM) Oldenburg, Germany.</p>
</blockquote>
<blockquote>
<p>He then became the Team Leader Peptidomics technology at BioVisioN (Hannover, Germany). In 2004 he joined Thermo Fisher Scientific as application/demo chemist, followed by various roles in Product Management.</p>
</blockquote>
<blockquote>
<p>Thomas is currently leading global Product Management efforts for Life Science Mass Spectrometry as Senior Director of Hardware Platform Management.</p>
</blockquote>
<blockquote>
<p><strong>Presenter: Helen Cooper (Professor of Mass Spectrometry, Deputy Head of School, EPSRC Established Career Fellow, Birmingham University)</strong></p>
</blockquote>
<blockquote>
<p>Professor Helen J. Cooper is an expert in the gas-phase ion chemistry of peptides and proteins. She is a world-leader in the field of electron capture dissociation mass spectrometry and is responsible for establishing the University of Birmingham as a centre of excellence in mass spectrometry research. Professor Cooper has published extensively in peer-reviewed journals and serves on a number of national and international committees including the Editorial Board for the Journal of the American Society for Mass Spectrometry and the British Mass Spectrometry Society.</p>
</blockquote>


Thermo Scientific: LC-MS User Meeting 2020 - Omics - Plenary Session

LC-MS User Meeting 2020 - Omics - Plenary Session

<p><strong>Proteomics and metabolomics have become widely adopted techniques, often multi-disciplinary, requiring the collaboration of biologists and medical doctors, of protein chemists, mass spectrometrists and bioinformaticians delivering the value of innovative applications and novel workflows as fresh knowledge on health, disease and biology. This field relies on the scientific community pushing the limits of mass spectrometry (MS) technology to gain understanding in various disease areas that can lead to effective diagnostics, treatments and vaccines. Over this day, we will highlight several of these cutting-edge developments and results in single cell analysis, spatial omics and clinical research deploying artificial intelligence for improved data acquisition and interpretation. Our specialists will also share their recommendations for achieving outmost performance with our instruments and software.</strong></p>
<h5><strong>11:00 BST (12:00 CEST - Prague) | Optimal workflows for spatial proteomics on the Orbitrap Eclipse Tribrid Mass Spectrometer</strong></h5>
<ul>
<li><strong>Speaker:</strong> Prof. Kathryn Lilley, Research Group Head, University of Cambridge, UK</li>
</ul>
<h5><strong>11:30 BST (12:30 CEST - Prague) | Pushing the Limits of Sensitivity: Micropillar Array-Based Chromatography Coupled to a Quadrupole Orbitrap Mass Spectrometer and FAIMS for Low-Input Proteomics</strong></h5>
<ul>
<li><strong>Speaker:</strong> Karl Mechtler, Head of Protein Chemistry Facility bei Research Institute of Molecular Pathology (IMP), Vienna Biocore Facilities, Austria</li>
</ul>
<h5><strong>12:00 BST (13:00 CEST - Prague) | Mass spectrometry-based draft of the Arabidopsis proteome (Mergner et al Nature 2020)</strong></h5>
<ul>
<li><strong>Speaker:</strong> Dr. Julia Mergner, Head of Proteomics, TU - Munich, Germany</li>
</ul>
<h5><strong>12:30 BST (13:30 CEST - Prague) | MS Based Approach for Low Amount Tissue Proteome Profile</strong></h5>
<ul>
<li><strong>Speaker:</strong> Alessandro Cuomo, Coordinator Mass Spectrometry Unit, IEO Research - Milano, Italy</li>
</ul>
<blockquote>
<p><strong>Presenter: Prof. Kathryn Lilley (Research Group Head, University of Cambridge, UK)</strong></p>
</blockquote>
<blockquote>
<p>Kathryn Lilley is a Professor in the Department of Biochemistry and a member of the Milner Therapeutics Institute.She is also Director of theCambridge Centre for Proteomics, and a Director of Studies at Jesus College.</p>
</blockquote>
<blockquote>
<p>Kathryn&#39;s research specialisesin the development of cutting edge proteomics technologies. Her research group is exploring waysto:</p>
</blockquote>
<ul>
<li>Defineresidents of organelles and protein complexes within cells</li>
<li>Usea combination of high throughput mass spectrometry and pattern recognition methods to define genuine residents of complexes and organelles</li>
<li>Monitor concerted changes in location upon cellular perturbation such as drug treatment, mutation etc.</li>
</ul>
<blockquote>
<p>These methods are being used to locate proteins involved in stem cell pluripotency maintenance both in terms of sub cellular location and involvement in multi protein complexes.</p>
</blockquote>
<blockquote>
<p>She is also interested in what controls the location of proteins in cells and is developing methods to determine the spatial location of translation (where proteins are synthesised).</p>
</blockquote>
<blockquote>
<p><strong>Presenter: Karl Mechtler (Head of Protein Chemistry Facility bei Research Institute of Molecular Pathology (IMP), Vienna Biocore Facilities, Austria)</strong></p>
</blockquote>
<blockquote>
<p>Main Research Areas</p>
</blockquote>
<ul>
<li>Major topics: Proteomics, Mass Spectrometry, Bioinformatics</li>
<li>Specialized in: Analysis of post-translational modifications, cross-linking mass spectrometry, single cell proteomics</li>
<li>Development of new mass spectrometry methods to increase sensitivity, accuracy and precision of protein identification and quantification.</li>
<li>Development of novel algorithms to increase the number of identified peptides, determine the localization of post-translational modifications and for label-free quantification.</li>
</ul>
<blockquote>
<p>Main Research Achievements</p>
</blockquote>
<ul>
<li>Establishment of the first Proteomics Core Facility in Austria in 2000, which is embedded in the Campus Vienna Biocenter and available to scientists from the Research Institute of Molecular Pathology (IMP), the Institute of Molecular Biotechnology (IMBA) and the Gregor Mendel Institute (GMI) today.</li>
<li>Development of methods for the analysis of post-translational modifications (phosphorylated arginine, glycoproteomics)</li>
<li>Development of different algorithms for qualitative and quantitative MS data analysis (available at http://ms.imp.ac.at), that are increasingly used by proteomics labs world-wide</li>
<li>(Co-)Author of more than 180 publications including contributions in Nature, Cell and Science.</li>
</ul>
<blockquote>
<p><strong>Presenter: Dr. Julia Mergner (Head of Proteomics, TU - Munich, Germany)</strong></p>
</blockquote>
<blockquote>
<p>I am a molecular biologist running a newly established proteomic competence center at the hospital campus of the TU Munich. I am applying label-free, tandem-mass-tag and targeted proteomic techniques to study global proteome expression, protein complex compositions and PTM site localizations. The aim of my research is to advance technologies for the detection and quantification of proteins and post-translational modifications using liquid-chromatography-based tandem mass spectrometry.</p>
</blockquote>
<blockquote>
<p>Career</p>
</blockquote>
<blockquote>
<p>Professional experience</p>
</blockquote>
<ul>
<li>2020 – present Head of Proteomics at the Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), TU Munich, Germany</li>
<li>2015 - 2020 Post-Doc at the Chair of Proteomics and Bioanalytics, TU Munich, Germany</li>
<li>Research project “The Arabidopsis proteome”, Proteomic Z-project coordinator for SFB924 “Molecular mechanisms regulating yield and yield stability in plants”</li>
</ul>
<blockquote>
<p>Education</p>
</blockquote>
<ul>
<li>2010 - 2015 PhD in Molecular Biology at the Chair of Plant Systems Biology, TU Munich, Germany</li>
<li>Project “Characterization of DENEDDYLASE1 function in Arabidopsis”</li>
<li>2004 - 2010 Biology training at the Albert-Ludwigs-University Freiburg i. Breisgau, Germany</li>
<li>Diploma thesis “Ontogenetic changes in biomechanics and functional morphology of weeping plants”</li>
</ul>
<blockquote>
<p><strong>Presenter: Alessandro Cuomo (Coordinator Mass Spectrometry Unit, IEO Research - Milano, Italy)</strong></p>
</blockquote>
<blockquote>
<p>Alessandro is the Head of <a href="https://www.research.ieo.it/research-and-technology/technological-units/proteomics-unit/">Mass Spectrometry Unit (MSU) at European Institute of Oncology (IEO), Department of Experimental Oncology (DEO).</a></p>
</blockquote>
<blockquote>
<p>Education and Training</p>
</blockquote>
<ul>
<li>January 2015: Staff Scientist at European Institute of Oncology (IEO)</li>
<li>April-October 2012: Visiting Scientist:Max Plank Institute (MPI)-</li>
</ul>
<blockquote>
<p>M. Mann Lab</p>
</blockquote>
<ul>
<li>October 2008: Post-Doc position: European Institute of Oncology (IEO).</li>
<li>October 2008: Doctor of Philosophy (PhD) in Molecular Medicine (SEMM program- http://www.semm.it).</li>
<li>April 2007- Sept. 2008: Visiting Scientist:Utrecht University (The Netherlands) - A. J. Heck Lab</li>
<li>January 2004-Dec. 2004: Temporary staff: CEINGE Biotechnology Institute, School of medicine Naples.</li>
<li>Oct. 2002-Dec. 2003: Temporary staff: DSTB School of medicine of Udine.</li>
<li>June 2002: B. Sc. (Laurea) Chemistry, University of Naples “Federico II”.</li>
</ul>


LCMS webinars focusing on LC/Orbitrap - page 17

LC-MS User Meeting 2020 - Omics/Proteomics Morning Session

LC-MS User Meeting 2020 - Omics - Plenary Session

Virtual seminar session 1: Impurity analysis with a focus on nitrosamines

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