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.<h4>In this episode, you'll learn:</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>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.<h4>Referenced Papers:</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>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.<h3>Video Transcription</h3><h4>From Structural Biology to Drug Discovery: Chromatography and Mass Spectrometry in Malaria Research</h4><h5>Introduction</h5>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.<h5>Research Focus: Malaria Drug Discovery and Kinase Targets</h5>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.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.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.<h5>Chromatography in Protein Expression and Purification Workflows</h5>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.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.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.<h5>Integrating Size Exclusion Chromatography into the Workflow</h5>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.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.These iterative purification and troubleshooting steps are a routine part of protein biochemistry and reflect the importance of methodical optimization and careful validation.<h5>The Role of Mass Spectrometry in Biomolecular Characterization</h5>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.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.These approaches are essential for understanding how candidate drug targets function within complex biological systems.<h5>Sample Preparation Challenges in Biological Research</h5>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.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.<h5>Advances in Chromatography and MS for Malaria Research</h5>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.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.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.<h5>Malaria, Drug Resistance, and Global Impact</h5>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.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.Understanding these molecular mechanisms is essential for developing robust, stage-specific antimalarial strategies.<h5>Advice for Early-Career Researchers</h5>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.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.Every successful experiment—no matter how small—represents meaningful progress and contributes to the broader goals of science and medicine.<h5>Closing Remarks</h5>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.<blockquote>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.</blockquote><blockquote><h4>Concentrating on Chromatography Podcast</h4>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!You can find Concentrating on Chromatography Podcast in podcast apps:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://open.spotify.com/show/1wZg67rCjoGju4yhqxI3tL">Spotify</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podcasts.apple.com/tz/podcast/concentrating-on-chromatography/id1788429185">Apple podcast</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podscan.fm/podcasts/concentrating-on-chromatography">podscan</a></li></ul>and on <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@ChromatographyTalk/videos">YouTube channel</a></blockquote>

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

In the week of February 9, the following webinars await you in the field of liquid phase and especially HPLC and LC/MS.<blockquote><h4><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinars">👉 DETAILS AND REGISTRATION IN THE WEBINARS SECTION</a></h4>👉 Search and filter in the largest global database with over 5 000 GC, LC, MS and spectroscopy webinars.</blockquote><h5>1. SelectScience: High-Throughput Stability Screening Strategies for Antibody Formulation</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>Learn how high-throughput DLS/SLS and rapid-screening DSC accelerate stability assessment of high-concentration antibody formulations, enabling faster, data-driven biologics development.<h5>2. Phenomenex: Big Scale, Big Wins – Prep Chromatography Explained</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>Learn how to scale analytical methods to preparative HPLC, optimize loading capacity, and understand the limits of preparative columns for pharmaceutical applications.<h5>3. ALS Czech Republic: PFAS in Food &amp; Food Contact Material</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>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.<h5>4. New Food Magazine: The Science of Next-Gen Ingredients – Fermentation, Formulation and Function</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>Explore how fermentation-driven innovation is transforming functional food ingredients and how advanced analytics optimize flavour, functionality, and stability.<h5>5. SCIEX: Accurate Mass Fundamentals – Interpreting and Applying Your Data</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>Session 3 focuses on interpreting and applying accurate mass data to confirm compound identity, move beyond basic quantitation, and troubleshoot results for confident reporting.<h5>6. Agilent Technologies: Process Analytical Techniques – Online HPLC for Real-Time Monitoring and Control of Bioprocesses</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>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.<h5>7. Thermo Fisher Scientific: Introducing the Orbitrap Excedion Pro Hybrid MS</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>Discover the new Orbitrap Exploris Pro with expanded ETD/EThcD capabilities for confident biopharmaceutical characterization, including intact proteins, PTMs, ADCs, and large biomolecules.<h5>8. Waters Corporation: Planning Your NuGenesis Upgrade – Insights and Best Practices for a Smooth Transition</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>Learn how to plan a successful NuGenesis upgrade, transition to Windows 11, and unlock new capabilities such as dashboards for real-time operational insights.<h5>9. Thermo Fisher Scientific: Comprehensive Analytical Strategies for Peptide Therapeutics and GLP-1 Agonists with Agilent</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>Explore analytical workflows for peptide therapeutics, including method development, peptide mapping, GLP-1 QC, and LC-MS strategies across Agilent platforms.<h5>10. Agilent Technologies: Moving from R&amp;D and Limited QC on a UV-Vis-NIR Instrument to Large-Scale QC Using an Autosampler</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>This webinar covers practical aspects of adding and using an autosampler to maximize UV-Vis-NIR QC workflows at scale.<h5>11. Agilent Technologies: LC Method Transfer – Hidden Challenges &amp; Absolute Solution</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>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.

Webinars LabRulezLCMS Week 07/2026

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.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.<blockquote><h4>The original article</h4><h4><a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05771">Dissecting Heterogeneous Populations of Protein-Complex Samples Using Direct Mass Technology</a></h4>Robert L. Rider, Jared Hampton, Zhenyu Xi, Carter Lantz, Sangho D. Yun, Weijing Liu, Rosa Viner, Arthur Laganowsky, and David H. Russell*Anal. Chem. 2025, 97, 49, 27057–27063<a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1021/acs.analchem.5c05771">https://doi.org/10.1021/acs.analchem.5c05771</a><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a></h6></blockquote>Selected sections from the article follow. Formats and hyperlinks were adapted from the original.Transthyretin (TTR) is a homotetrameric transport protein that circulates in plasma and cerebrospinal fluid, delivering thyroxine (T4) 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.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>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 m/z 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 m/z 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>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 (m/z × 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.<h4>Experimental Section</h4><h5>Data Collection</h5>All experiments were conducted on a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/560">Thermo Scientific Q-Exactive UHMR</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.<h4>Results and Discussion</h4>CDMS has emerged as a powerful tool for analyzing heterogeneous biomolecular samples, enabling accurate, direct mass determination by simultaneously measuring the charge and m/z 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 m/z). <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 T4 bound states of both WT- and CT-TTR tetramers, where &lt;3900 m/z has observable separation between all proteoforms. However, for the 14+ and 15+ charge states of WT- and CT-TTR, respectively, the 0 T4- and 1 T4-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+, K+, and Zn2+) 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 m/z overlap to resolve and quantify hybrid tetramer formation and T4 binding.<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"><h5>Thyroxine Binding to TTR Homotetramers</h5>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 T4 into T3 (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 T4 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 T4) 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 T4.DMT was further applied to quantify T4 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 T4. While ligand-bound species can be observed, homotetramers cannot be confidently resolved across the entire 3000–5000 m/z 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 m/z by separating the 14+ and 15+ charge states for WT and CT, respectively, in the range 3900–4200 m/z. 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 m/z yet differ in mobility, CDMS could be an alternative or used complementarily since the species likely also differ in charge.<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"><h4>Conclusion</h4>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 T4 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.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 m/z 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 m/z 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>

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

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DataApex Clarity Offline Chromatography Software

Clarity Offline allows users to import previously acquired data and to evaluate and prepare methods in regulated environment.

Clarity Offline allows users to import previously acquired data and to evaluate and prepare methods. This version cannot acquire data, but it can share data or even directly access (through LAN) projects of the <a href="https://lcms.labrulez.com/products/999">Clarity</a> and Clarity Lite software. With Clarity Offline users are able to work with acquired data on additional computers in the lab or at home. The software works with the same files and provides the same outputs (printing and exporting) as Clarity and Clarity Lite.
Clarity Offline is intended for use as additional software that supplements Clarity and Clarity Lite. It can also be used to evaluate data from other manufacturers&#39; CDS.
<blockquote>
Ask for <a href="https://www.dataapex.com/product/clarity-demo">Clarity Demo version</a> which allows you to get your hands on software before purchase
</blockquote>
<h3>Main features</h3>
<ul>
<li>21 CFR Part 11 compliance: Clarity Offline contains all functions (Electronic Signatures, User Accounts, Audit Trail, etc.) for compliance with the 21 CFR Part 11 directive of the FDA. Clarity Offline can be used for evaluation in regulated environments.
</li>
<li>Networked Solution: Clarity Offline can access files of Clarity and Clarity Lite installed on networked computers. This enables evaluation of chromatograms, development of new methods, and printing reports on additional computers in the laboratory.
</li>
<li>Education: An additional field of use is in education. Students can process chromatograms that have been acquired from Clarity connected to a chromatograph using their Clarity Offline license. Thus they do not need a Clarity full license just for data evaluation.
</li>
<li>Data processing and evaluation from other chromatography software: Clarity Offline allows the import of data from other chromatography software using text or AIA import function. This allows the user to process and evaluate chromatograms acquired by other chromatography software.
</li>
<li>Offsite computer: Clarity Offline can be installed on any Windows computer, giving you anytime access to your chromatographic data (USB hardware key is required).
</li>
<li>Language Localizations available: Useful for non-English speakers. At the moment, there are French, German, Russian, Spanish, and Chinese localizations available in a single installation package. Simply switch to your preferred language anytime.
</li>
</ul>
<a href="https://www.dataapex.com/controls">List of supported instruments</a>
<a href="https://www.dataapex.com/product/clarity-std-compatibility">Compatible Windows OS and Hardware</a>
<a href="https://www.dataapex.com/product/clarity-21cfr-compliance">Clarity 21 CFR Part 11 compliance</a>

DataApex PDA - Photodiode Array Extension for Clarity

The PDA Extension is an optional Extension that is used for processing data that has been acquired from selected photo diode array detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis.

<h3>Extension for 3D data analysis from Photodiode Array Detectors</h3>
The PDA Extension is an optional Extension that is used for processing data that has been acquired from selected photo diode array detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis. This extension expands the capability of <a href="https://lcms.labrulez.com/products/999">Clarity</a> by providing interactive spectral analysis, peak purity analysis and compound identification that is based on a spectral library search. PDA data can be displayed in a set of optional views including 3D rendering.
All data is saved in a single file; a chromatogram at any wavelength or even only a spectrum can simply be recalled for review after an analysis. UV-VIS spectra, acquired using a PDA detector, may be interactively selected from a chromatogram signal for visual inspection and comparison. The spectra may also be used for peak purity determinations, wavelength optimization and component identification through spectral libraries.
<h4>Main features</h4>
<ul>
<li>PDA View: The PDA view is customizable; up to four views can be displayed at one time (Any combination from the following views may be selected: Isoplot, Chromatogram, Spectra, 3D Display, Peak Purity, Peak Purity Spectra, Library Spectra Search and Spectral Library). The user can easily extract chromatographic signals from PDA data to determine the optimal detection wavelength for each peak.
</li>
<li>PDA Method: The Clarity PDA method includes an option for Spectral Library Search and Peak Purity analysis.
</li>
<li>Limit values: These calculated values are compared to user-set limit values, either for each chromatogram separately or together for the selected series. Deviation of a certain parameter from the permissible limits is immediately reported and may lead to the termination of the sequence in progress.
</li>
<li>Spectral Library: The Clarity software compares the peak spectra with the spectra of an unlimited number of spectral libraries. Spectra stored in a Spectral Library include retention times and analysis parameters (optional). The Spectral Library Search can perform automatic identification of integrated/calibrated components (peaks). The library search may be constrained by the RT Window and by Wavelength Range. Either the Least Square, the Weighted Least Square or the Correlation Method is used for calculating library search matches. A Background Correction option is also available.
</li>
<li>Peak Purity: This analysis helps to discover hidden impurities. Peak Purity test is applied to all integrated/calibrated peaks in the active signal. Purity is calculated from 5 or all spectra within the peak. The similarity curve is displayed in the PDA window. Peak Purity analysis can be optimized by setting custom preferences relating to the purity threshold, wavelength restriction and absorbance threshold.
</li>
<li>Import/Export Data: Spectral data can be imported/exported in ASCII text formats to or from the <a href="https://lcms.labrulez.com/products/999">Clarity software</a>.
</li>
<li>Reports: Users can easily include PDA options such as data 3D Display, Isoplot, Spectra, Peak Purity and Library Search results in reports using the intuitive Report Setup Dialog.
</li>
<li>Instrument Control: Control modules for Agilent 1100 DAD and FLD, Sykam S3210/3240, Knauer PDA and many others are available. Additional control modules for other PDA detectors can be developed upon request.
</li>
</ul>
<a href="https://www.dataapex.com/controls#9709a8ca9130f20fc18c284302efd33b">List of controlled PDA detectors</a>

DataApex SST - System Suitability Test Extension for Clarity

The SST extension serves to monitor the correct function of the chromatography system. The program compares up to 12 selected parameters (e.g., retention time, efficiency, asymmetry of peaks) calculated according to one of three pre-selected methods (USP, EP, JP).

<h3>The SST extension serves to monitor the correct function of the chromatography system.</h3>
The program compares up to 12 selected parameters (e.g., retention time, efficiency, asymmetry of peaks) calculated according to one of three pre-selected methods (USP, EP, JP). These calculated values are either compared to the user&#39;s set limit values for each chromatogram separately or together for the selected series. Deviation of any parameter from the permissible limits is immediately reported and may lead to the termination of the sequence in progress. The SST Extension allows the user to monitor the parameters of individual substances and thus evaluate the reproducibility of the results of the entire chromatography system.
The SST extension is required when using the <a href="https://www.dataapex.com/product/validation-kit">Validation Kit</a>.
<h3>Main features</h3>
<ul>
<li>Measuring: Simultaneous data acquisition from up to four signals (detectors) attached to one chromatograph.
</li>
<li>Parameters: The program compares up to 12 selected parameters (e.g., retention time, efficiency, asymmetry of peaks) calculated according to one of three pre-selected methods (USP, EP, JP).
</li>
<li>Limit values: These calculated values are compared to user set limit values, either for each chromatogram separately or together for the selected series. Deviation of a certain parameter from the permissible limits is immediately reported and may lead to the termination of the sequence in progress.
</li>
<li>Versatility: Even though validation primarily focuses on testing system reliability, it can also be used in many other ways. Validation can be run during measurements, or additionally, using batch processing. Validated data can be automatically saved to a database file for further processing.
</li>
<li>Enhanced sequencing: In connection with a sequence, the SST module can even pause a sequence when a specified value has been exceeded or to perform predefined functions.
</li>
</ul>
<a href="https://gcms.labrulez.com/products/999">Clarity</a> Chromatography Software required

DataApex MS - Mass Spectrometry Extension for Clarity

The Clarity MS Extension is a tool that is used for processing data that has been acquired from selected Mass Spectrometry detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis.

<h3>Clarity Extension for processing data that has been acquired from selected Mass Spectrometry detectors</h3>
The Clarity MS Extension is a tool that is used for processing data that has been acquired from selected Mass Spectrometry detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis.
The MS Extension expands the capability of <a href="https://lcms.labrulez.com/products/999">Clarity</a> and <a href="https://lcms.labrulez.com/products/1000">Clarity Offline</a> Chromatography software by providing interactive spectral analysis, peak purity analysis, and compound identification that is based on a spectral <a href="https://gcms.labrulez.com/products?category=249">library</a> search. The extension is prepared to function with single quadrupole MS detectors and TOF MS detectors.
All data is saved in a single file; a chromatogram at any m/z value or even only a spectrum can simply be recalled for review after an analysis. MS spectra, acquired using an MS detector, may be interactively selected from a chromatogram signal for visual inspection and comparison. The spectra may also be used for peak purity determinations and component identification through spectral <a href="https://lcms.labrulez.com/products?category=285">libraries</a>.
It is possible to import MS data in AIA (cdf), mzXML, MzML, and mzData formats.
Control modules for selected detectors (see <a href="https://www.dataapex.com/controls">list of control modules</a>) are available in Clarity. Additional control modules for MS detectors can be developed upon request.

DataApex GPC - Gel Permeation Chromatography Extension for Clarity 

GPC Extension provides interactive and automated GPC analysis, including recalibration and GPC reporting, as well as simplifies the retrieval of GPC data. The GPC Extension allows flow rate and multi-detector delay corrections and includes Narrow, Broad, and Broad on Narrow calibrations.

<h3>Extension provides interactive and automated GPC analysis, including recalibration and GPC reporting, as well as simplifies the retrieval of GPC data.</h3>
Gel Permeation Chromatography (GPC) / Size Exclusion Chromatography (SEC) is the technique used for obtaining a rapid and reliable characterization of polymer molecular weight and molecular weight distribution. GPC Extension provides interactive and automated GPC analysis, including recalibration and GPC reporting, as well as simplifies the retrieval of GPC data. The GPC Extension allows flow rate and multi-detector delay corrections and includes Narrow, Broad, and Broad on Narrow calibrations.
<h3>Main features</h3>
<ul>
<li>Data Acquisition: Simultaneous data acquisition from up to four four-detector chromatographs (4×4 configuration), detector delay correction for multidetector measurement. 
</li>
<li>Data Processing: The same chromatograms can be evaluated in both standard and GPC modes. Multiple peaks and multiple signals are processed in one chromatogram.
</li>
<li>GPC Integration: Separate integration tables for GPC and standard evaluation are used. There are extensive possibilities for modifying chromatograms. The chromatogram integration can be changed by entering global parameters or interactively, through the direct graphical modification of the baseline.
</li>
<li>Calibration: Narrow, Broad, Broad on Narrow standard calibration methods combined with Flow Rate correction and Universal calibration. Manual calibration or automated recalibration from a sequence. Multiple Broad standards can be used.
</li>
<li>GPC Calculations: Polynomial (n= 1-5) curve fits (independent for signals), Mp, Mn, Mw, Mv, Mz, Mz+1 molecular weight averages and polydispersity.
</li>
<li>Graphs: Molecular weight distribution graphs. Overlay: Simultaneously displays a virtually unlimited number of chromatograms. Overlay of dW/d logM vs. log M and cumulative height graphs.
</li>
<li>Export: Slice Table results, graphs, result and summary tables.
</li>
<li>User Calculations: Users can define custom calculations in the Result and Summary tables. Using the integrated editor, you can create your own columns from the original columns and individual mathematical functions.
</li>
<li>GPC Results Table: Displays molecular weight averages together with peak details for active signal. Multiple peaks can be evaluated from one chromatogram.
</li>
<li>GPC Summary Result Tables: Displays and prints selected results from all simultaneously displayed chromatograms. Postrun: Automatically displays, prints, exports, and starts other programs after the completion of a measurement.
</li>
<li>Batch: Automatically batch processes, displays, exports, or prints any number of chromatograms.
</li>
<li>Reports: User selectable report sections and WYSIWYG formating of Graphs and Tables.
</li>
</ul>

DataApex CE - Capillary Electrophoresis Extension for Clarity

CE module provides specific terminology, evaluation by time corrected area and peak identification by peak start or end (additionally to peak apex).

<h3>Extension for Capillary Electrophoresis</h3>
The CE Extension activates the CE mode in Clarity environment and can be activated on any <a href="https://lcms.labrulez.com/products/999">Clarity</a> Instrument. CE Extension is compatible also with <a href="https://lcms.labrulez.com/products/1000">Clarity Offline</a> software. CE module provides specific terminology, evaluation by time corrected area and peak identification by peak start or end (additionally to peak apex).
<h4>Main changes in Clarity environment</h4>
<ul>
<li>CE specific terminology</li>
<li>Evaluation by time corrected area</li>
<li>Peak identification by peak start or end (additionally to peak apex).</li>
<li>Additional calculations</li>
</ul>
<h4>CE specific terminology</h4>
The terms used in chromatography mode were substituted by those used in CE:
<ul>
<li>Default mode =&gt; CE mode</li>
<li>Chromatogram =&gt; Electropherogram</li>
<li>Retention time (RT) =&gt; Migration Time (MT)</li>
<li>Column =&gt; Capillary</li>
<li>Mobile Phase =&gt; Electrolyte</li>
<li>Flow Rate =&gt; Power supply</li>
<li>Pressure =&gt; Injection Mode</li>
</ul>
<h4>Separation parameters</h4>
Method Setup allows a user to adjust the Capillary Setting:
<ul>
<li>Total Capillary Length</li>
<li>Length of the capillary.</li>
<li>Effective Capillary Length</li>
<li>Effective capillary length from injection end to the detector position</li>
<li>Separation Voltage</li>
<li>Separation voltage. Allows you to enter also negative values</li>
<li>Reference Peak Mobility</li>
<li>Effective mobility of the EOF reference peak.</li>
</ul>
<h4>Calculations</h4>
The Result Table contains additional columns containing calculations:
<ul>
<li>Apparent Mobility</li>
<li>Effective Mobility</li>
</ul>

Watrex Streamline OLE 200 On-line SPE system

An automatic on-line solid-phase extraction (SPE) and pre-concentration unit with a 10-port selection valve processes up to 7 samples through 7 SPE cartridges. After washing, the eluted components are directed into an HPLC system via a sample valve. 

Automatic on-line SPE/pre-concentration unit equipped with 10 port selection valve for samples and washing solvents, high pressure cartridge selector for 7 cartridges, high pressure pump, and injection valve connected to HPLC instrument.The pump sucks through 10 port selection valve up to 7 samples to 7 SPE cartridges. Then collected components are washed with one or two slushing eluents, and eluted via sample valve into a HPLC system.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Watrex_Watrex_Streamline_OLE_200_On_line_SPE_system_Principle_of_online_SPE_by_OLE_200_e40db78c8f.jpg" alt="Watrex - Watrex Streamline OLE 200 On-line SPE system - Principle of online SPE by OLE 200"><h3>TECHNICAL SPECIFICATION</h3><ul><li>Cartridge selector: twin 10-port high pressure selector, 40MPa</li><li>Cartridge dimensions: 10x4mm</li><li>Connection to HPLC instrument: Rheodyne 6 port sample valve</li><li>Selector: low-pressure 10-port selection valve IDEX</li><li>Sample load pump: high-pressure single piston ss pump</li><li>Instrument control: driver for all valves and pump controll included</li></ul><h3>Ordering information:</h3><h5>PN/Component:</h5><ul><li>D2K2062401 Watrex OLE200</li></ul>You can also visit this product on the <a target="_blank" rel="noopener noreferrer" href="https://watrex.com/obchod/laboratory-automation/streamline-ole-200/?utm_source=labrulez&amp;utm_medium=propagace&amp;utm_campaign=labrulez_produkty">Watrex website</a>.

Watrex Streamline™ P1 HPLC Pump, Stainless Steel

The Watrex Streamline™ P1 pump is a versatile and powerful dual-piston HPLC pump.

Streamline P1 pump, stainless steel fully meets the demanding requirements for HPLC pumps and can be combined seamlessly with HPLC detectors and instruments from other manufacturers.<blockquote>Price 4 935 € ex VAT</blockquote>In the analytical version of the pump, the flow rate range from 0.001 ml/min to 10 ml/min is adjustable in 1 ul increments with a maximum working pressure of 42 MPa (6,000 psi). Flow rate adjustment accuracy is ±1% and flow rate variation is better than ±0.1%. The pump’s extremely smooth flow profile is ensured by an efficient pulse damper and optimized cam shape.A unique feature is the active piston and seal rinse, which prevents crystallization of buffers. A touch screen display on the front panel allows intuitive control of the pump.The display shows the flow rate, the current pressure and the pump is equipped with pressure limits. A PRIME function is also directly available for flushing at increased flow rates.<figure class="image"><img style="aspect-ratio:611/408;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Watrex_Streamline_P1_Pump_Stainless_Steel_23a7bf9f11.jpg" alt="Watrex: Streamline™ P1 Pump, Stainless Steel." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Watrex_Streamline_P1_Pump_Stainless_Steel_23a7bf9f11.jpg 234w," sizes="100vw" width="611" height="408"></figure><h3>TECHNICAL SPECIFICATION</h3><ul><li>Flow Rates: 0.001 to 10.000 mL/min</li><li>Pressure: 0 to 6,000 psi (42 MPa)</li><li>Flow precision: &gt; 0.2% RSD</li><li>Flow accuracy: ± 1 % @ 1mL/min and 7 MPa,</li><li>Pressure accuracy: ± 2% of full-scale, with 80:20 H2O/IPA @ 7 MPa</li><li>Pulsation: ± 0.5 % @ 1mL/min and 7 MPa</li><li>Remote inputs: USB</li></ul>You can also visit this product on the <a target="_blank" rel="noopener noreferrer" href="https://watrex.com/obchod/chromatography/pumps/isocratic-pumps/streamline-p1-pump-stainless-steel/?utm_source=labrulez&amp;utm_medium=propagace&amp;utm_campaign=labrulez_produkty">Watrex website</a>.

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