Exploring the Impact of Two DNA Minor Groove Binder Compounds on HCT-116 Cells: A Comprehensive Multiomics Analysis Using Mass Spectrometry
Colorectal cancer (CRC) remains a major global health burden, necessitating innovative therapeutic approaches with improved selectivity and reduced toxicity. DNA minor groove binders (MGBs) represent a promising class of agents that modulate DNA-associated processes without inducing permanent DNA damage. In this study, two previously reported distamycin-like DNA minor groove binders, MGB30 and MGB32, were investigated to elucidate their molecular mechanisms of action in HCT-116 human colorectal cancer cells. An integrated multiomics approach combining metabolomics and proteomics was employed using TIMS-QTOF-UHPLC-MS. Four biological replicates were used for each treatment condition. Following MGB30 treatment, 12 metabolites and 187 proteins were significantly dysregulated, whereas MGB32 treatment resulted in alterations of 41 metabolites and 409 proteins using a Student’s t-test with q-value <0.05. Pathway enrichment analysis revealed that both compounds significantly disrupted purine metabolism, while MGB32 additionally affected beta-alanine metabolism, glutathione metabolism, and spermidine and spermine biosynthesis. Proteomic analysis further demonstrated deactivation of RNA processing, translation, and ribosome biogenesis, leading to impaired protein synthesis and reduced cancer cell proliferation. This study provides mechanistic insights into the downstream molecular effects of MGB30 and MGB32 that disrupt key mechanisms underlying tumor growth, offering new avenues for CRC treatment.
Exploring the Impact of Two DNA Minor Groove Binder Compounds on HCT-116 Cells: A Comprehensive Multiomics Analysis Using Mass Spectrometry #JProteomeRes pubs.acs.org/doi/10.1021/...
06.03.2026 19:20
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Presence of Emerging Contaminants in UK Honey─Human Pharmaceuticals a Concern for Honeybees?
Emerging contaminants can accumulate in water, soils, and crops; however, little is known about the potential exposure to honeybees. Using samples collected surrounding arable farming in Great Britain and nontarget techniques, we identified 119 suspect chemicals in hives. On average, each hive contained 6.8 (±3.01) active ingredients, these included human pharmaceuticals (64%), industrial chemicals (10%), surfactants (8%), and plasticizers (5%). Elevated concentrations of the anti-inflammatory flurandrenolide (582.3 ± 348.4 ng/g), the nonsteroidal anti-inflammatorydrug aspirin (358.2 ± 390.1 ng/g), the fungicide azoxystrobin (298.5 ± 159.9 ng/g), the antihypertensive methyldopa (123.4 ± 60 ng/g), and the anticonvulsant carbamazepine (79.97 ± 54.2 ng/g) were identified. Elevated concentrations of human-origin contaminants of emerging concern (CECs), and their increased frequency in arable areas, indicate that the reuse of contaminated fertilizers contributes to accumulation in hives across English landscapes. Critically, most of these contaminants lack toxicity data for honeybees, making it impossible to assess their acute or chronic risks.
Presence of Emerging Contaminants in UK Honey─Human Pharmaceuticals a Concern for Honeybees? #JAFC #MassSpec pubs.acs.org/doi/10.1021/...
06.03.2026 10:07
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Assessing Digestive Transformations of Withania somnifera Extracts via LC–MS/MS Profiling with a Focus on Bioactive Compounds Withaferin A, Withanolide A, Withanoside IV, and Untargeted Metabolomics
Botanical extracts are widely employed as health care agents but lack the rigorous vetting required for FDA-approved pharmaceuticals. Research on phytochemical bioavailability and transformation has mainly focused on liver metabolism and plasma binding, while gastrointestinal and microbiome metabolism studies remain limited. This study combined digestive in vitro assays with mass spectrometry-based metabolomics and molecular networking to analyze metabolites in Withania somnifera leaf and root extracts, along with three known bioactive reference standards: withaferin A, withanolide A, and withanoside IV. Both withaferin A and withanoside IV underwent significant in vitro transformation, while withanolide A remained stable across conditions. Molecular networking revealed that withanolides in the root extract were largely stable, whereas many in the leaf extract were more labile under the assay conditions. Detailed network analysis also enabled the identification of specific metabolite transformations. These findings support the refinement of in vitro models to better predict in vivo behavior in complex botanical mixtures.
Assessing Digestive Transformations of Withania somnifera Extracts via LC–MS/MS Profiling with a Focus on Bioactive Compounds Withaferin A, Withanolide A, Withanoside IV, and Untargeted Metabolomics #JAFC pubs.acs.org/doi/10.1021/...
05.03.2026 14:59
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Integrating Ion Beam Control into a Commercial Platform for Improved Multimodal SIMS/MALDI Imaging
Mass spectrometry imaging (MSI) provides spatially resolved chemical analysis of surfaces and is widely applied in biological and biomedical research. Multimodal MSI can combine techniques such as secondary ion mass spectrometry (SIMS) and matrix-assisted laser desorption/ionization (MALDI) to leverage their complementary strengths. However, acquiring multimodal MSI data using separate instruments introduces challenges, including image coregistration and potential sample degradation during transfer. To address these limitations, we previously integrated a C60 ion gun into a prototype, commercially available MSI instrument, enabling SIMS, MALDI, and secondary electron imaging within a single platform. In this study, we implemented field of view (FoV) mode SIMS on this platform by rastering the ion beam, achieving an improved spatial resolution of 2 μm and surpassing the spatial resolution of the sample stage. Additionally, we optimized the instrument for elemental ion signals and observed enhanced sensitivity of selected species in SIMS through collision-induced dissociation (CID). To explore the usability of the ion gun for high-spatial-resolution image coregistration with other imaging modalities, fiducial markers were etched using the ion gun, creating a localized absence of signal in the etching locations, which can aid coregistration with optical imaging. Additionally, the secondary electrons produced by rastering the ion beam were used to image and assess the MALDI laser focus and power, allowing us to determine the optimal settings.
Integrating Ion Beam Control into a Commercial Platform for Improved Multimodal SIMS/MALDI Imaging #JASMS pubs.acs.org/doi/10.1021/...
05.03.2026 14:58
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Optimization of the Identification Rate and Reproducibility of an Untargeted diaPASEF Method Applicable for Quantitative Peptide Profiling of Hydrolyzed Infant Formula
Quality control of hydrolyzed infant formula (HIF) requires comprehensive and precise quantification of its peptide components. Quantitative peptidome analysis by liquid chromatography–tandem mass spectrometry (LC–MS/MS) with data-independent acquisition (DIA) and parallel accumulation–serial fragmentation (PASEF) is used for this application. Here, an optimization strategy was developed to increase the peptide identification rate and the qualitative and quantitative reproducibility of this approach. To expand the peptide identification rate, the originally assigned equidistant ion mobility (IM) windows were transferred to variable ion mobility windows with manually adjusted window placement. To improve the reproducibility, major acquisition parameters, such as the number of diaPASEF scans and ion mobility windows as well as the resulting cycle time, were systematically optimized. Thus, the approach was modified from 17 equidistant windows with a cycle time of 1.8 s to 30 variable windows with a cycle time of 1.7 s. The optimization process led to the identification of 628 peptides versus 522 peptides, increasing the identification rate by 20.3%. Concurrently, the coefficient of variation (CV) for peptide identification was reduced from 10.9 to 0.8%, and for quantitative reproducibility, it was reduced from 24.3 to 17.2%. Based on these results, an optimization workflow is presented to systematically improve the identification rate and reproducibility for other sample types and instruments.
Optimization of the Identification Rate and Reproducibility of an Untargeted diaPASEF Method Applicable for Quantitative Peptide Profiling of Hydrolyzed Infant Formula #JProteomeRes pubs.acs.org/doi/10.1021/...
04.03.2026 19:25
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Advancing Collision-Induced Affinity Selection Mass Spectrometry for Quantitative Ligand Analysis in Complex Mixtures
Native mass spectrometry (MS) is a powerful technique for studying protein–ligand interactions in their native states by employing soft electrospray ionization (ESI). It enables the direct observation of all species in equilibrium within a solution. Building on these advantages, Collision-Induced Affinity Selection MS (CIAS-MS) was introduced as an alternative approach, incorporating quadrupole mass selection, controlled complex dissociation, and ligand detection to enhance the study of protein–ligand interactions. This method retains the native ionization properties of proteins while enabling high-sensitivity detection of released ligands. This study presents an optimized CIAS-MS platform for improved ligand binding detection and quantitative affinity ranking. The integration of both positive and negative ion modes significantly broadens the detection of structurally diverse ligands, overcoming biases from single-mode analysis. More importantly, the collision-induced dissociation (CID) slope, derived from dissociation curves, is introduced as a robust parameter for affinity ranking. Unlike absolute intensities or dissociation thresholds, the CID slope reflects solution-phase affinity order across ligands and remains accurate in highly complex backgrounds, including 100-compound mixtures and bacterial lysates. These advances highlight the robustness of CIAS-MS for detecting bound ligands and ranking their affinities even under challenging conditions where traditional native MS fails. These findings establish CIAS-MS as a scalable and efficient platform for high-throughput ligand discovery and proteome-wide target engagement studies, offering a powerful addition to the biophysical toolkit for modern drug discovery.
Advancing Collision-Induced Affinity Selection Mass Spectrometry for Quantitative Ligand Analysis in Complex Mixtures #AC pubs.acs.org/doi/10.1021/...
04.03.2026 19:23
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Spatial Neurobiology in Brain Organoids Using Mass Spectrometry Imaging-Based Multiomics Approach
Brain organoids are stem cell-derived, three-dimensional models that more accurately mimic the cellular complexity and architecture of human brain tissues compared to traditional two-dimensional (2D) cultures or animal models. Their physiological relevance and human-specific neurobiology enhance translational research while aligning with current regulatory shifts toward reducing animal testing in biomedical science. A thorough understanding of the molecular landscape of various biomolecules, such as lipids, metabolites, proteins, and glycans in physiologically relevant brain models, such as organoids, is essential to deciphering complex neurobiology. While mass spectrometry has long been used to understand such molecular landscape in tissues, a single-omics approach is insufficient to fully capture the complexity of brain biology. Therefore, multiomics strategies, such as high-resolution mass spectrometry imaging (MSI), mass spectrometry-based proteomics, and lipidomics, together can provide a holistic view of biomolecular interplay within tissue microenvironments. Moreover, since MSI retains spatial information within tissues, MSI-based multiomics approaches hold immense potential to uncover complex neurobiology within brain organoids. In this article, we present our perspectives on leveraging MSI-based multiomics in brain organoids to understand the complex molecular interplay underlying neurobiology.
Spatial Neurobiology in Brain Organoids Using Mass Spectrometry Imaging-Based Multiomics Approach #ACSChemNeurosci pubs.acs.org/doi/10.1021/...
03.03.2026 13:29
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Diagnosing melioidosis and tracking treatment outcomes using breath
Diagnosing melioidosis and tracking treatment outcomes using breath, Gao, Antao, Mayo, Mark, Woerle, Celeste, Currie, Bart, Hill, Jane E
Diagnosing melioidosis and tracking treatment outcomes using breath #JBreathRes #MassSpec iopscience.iop.org/article/10.1...
03.03.2026 13:28
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