bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2025–12–21
38 papers selected by
Sofia Costa, Matterworks
  1. Advancing spatial-omics through Pyxis, vendor-neutral software for ion mobility mass spectrometry imaging data analysis.
  2. Simultaneous Determination of Thioridazine and Its Metabolites by UHPLC-MS/MS With Application to a Pharmacokinetic Study in Rats.
  3. A Taguchi Design of Experiments Approach for Untargeted Metabolomics Sample Preparation Optimization.
  4. VirMolAnalyte: An AI-Driven In Silico Metabolite Annotation Tool.
  5. [Simultaneous Analysis of Microcystins, Cylindrospermopsin, Anatoxin, and Nodularin in Lake Water by Liquid Chromatography-Tandem Mass Spectrometry].
  6. Comprehensive preclinical pharmacokinetics and metabolite profiling of a novel caspase inhibitor F573.
  7. Assessment of the benefits of adding differential mobility spectrometry to LC-MS/MS workflows for challenging steroid measurements.
  8. In-Source Fragmentation Annotation in Sterol Mass Spectrometry Imaging.
  9. Quantitative analysis of phylloquinone (vitamin K1) and menaquinone (vitamin K2) in serum of Russians by liquid chromatography-tandem mass spectrometry.
  10. Development and validation of a candidate reference measurement procedure for free triiodothyronine and free thyroxine in human serum using equilibrium dialysis isotope-dilution liquid chromatography-tandem mass spectrometry.
  11. An Analytical Perspective on Liquid Chromatography-Mass Spectrometry Methods for the Analysis of Bile Acids in Human Blood Samples.
  12. Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites.
  13. Recent advances in mass spectrometry-based bioanalytical methods for endogenous biomarkers analysis in transporter-mediated drug-drug interactions.
  14. Overcoming the Challenge of Confident Identification Among Two Related Groups of 17-Methyl Steroids by GC-MS.
  15. Analysis of propranolol and its metabolites in postmortem human solid tissues and body fluids: LC-MS/MS approach with the standard addition method applied to a forensic case.
  16. Epoxidation-Enhanced Charge-Switch Derivatization for Rapid Profiling of Monounsaturated Fatty Acid Isomers.
  17. [High-Throughput Determination of Endogenous Peptides in Urine Using Electromembrane Extraction Combined With Liquid Chromatography-Tandem Mass Spectrometry].
  18. Longitudinal, intra-individual stability of untargeted plasma and cerebrospinal fluid metabolites.
  19. [Determination of 18 Perfluorinated Compounds in Tea Leaves by a Quick, Easy, Cheap, Effective, Rugged, and Safe Method Combined With Ultra-High Performance Liquid Chromatography-Tandem Mass Spectrometry].
  20. mzLearn as a data-driven LC/MS signal detection algorithm that enables pre-trained generative models for untargeted metabolomics.
  21. Quantitative determination of suvorexant, lemborexant, and daridorexant in human plasma using a MonoTip C18 and gas chromatography-mass spectrometry.
  22. Simultaneous determination of vitamin B12 and cobalt (II) in infant milk power using liquid chromatography-inductively coupled plasma mass spectrometry.
  23. Bioanalytical method development for polmacoxib in rat plasma using LC-MS/MS and Its preclinical pharmacokinetic evaluation.
  24. LC-MS/MS and GC-MS Analysis-Based Novel Bioactive Compounds From Endophyte Acremonium sclerotigenum CBS 124.42 Isolated From Stevia rebaudiana (Bertoni) Bertoni.
  25. Coupling Liquid Chromatography to Orbitrap Isotope Ratio Mass Spectrometry: Overcoming Isotope Effects of Chromatography and Amount-Dependency by Peak Homogenization.
  26. LCMSpector: A simple open-source viewer for targeted hyphenated mass spectrometry analysis.
  27. Quantitative profiling of aromatic amino acids and their host-microbial co-metabolites in human urine via UPLC-MS/MS.
  28. Structure characterization with NMR molecular networking.
  29. Bioanalytical HPLC Method for Quantification of Benidipine in Rat Plasma: Stability and Application to Pharmacokinetic Study.
  30. Online Electroextraction-NanoESI-MS for Rapid Analysis of Catecholamines in Urine.
  31. Determination of Analytical Interferences for 4:2 Fluorotelomer Sulfonic Acid in Multiple Agricultural Matrices.
  32. Estrogen profiling in blood and brain: Effects of season and an aggressive interaction in a songbird.
  33. A Simple Online Internal Standard Calibration Strategy for Single-Particle Inductively Coupled Plasma Mass Spectrometry Based on Multielement Analysis.
  34. Rapid quantitation of NAD+/NADH and NADPH/NADP+ with mass spectrometry by using calibration constants.
  35. [High-Throughput Detection of Multiple Classes of Antibiotics in Source Water Using a Functionalized Polyacrylonitrile Nanofiber Membrane].
  36. Ensuring pharmaceutical safety: Highthroughput LC-MS/MS method for plastic additive detection.
  37. OmicsQ: A User-Friendly Platform for Interactive Quantitative Omics Data Analysis.
  38. Analytical methods and tools for studying inositol phosphates.
  1. Anal Bioanal Chem. 2025 Dec 20.
    Advancing spatial-omics through Pyxis, vendor-neutral software for ion mobility mass spectrometry imaging data analysis.
    Sara Tortorella, Sebastian Bessler, Giuseppe Arturi, Giulia Sorbi, Jens Soltwisch, Gabriele Cruciani.
      Mass spectrometry imaging (MSI) is a powerful analytical technique suited for simultaneously measuring and assigning functional roles of multiple analytes directly from intact tissue sections. MSI acquisitions often lead to highly complex datasets with numerous isobaric species. Ion mobility (IM) spectrometry crucially helps to unravel these datasets by providing an orthogonal separation thus supplementing the lack of chromatographic separation in MSI. However, the rich, multidimensional data produced by IM-MSI investigations, combined with the lack of comprehensive software solutions that support the entire data analysis workflow, poses a major challenge preventing IM-MSI full exploitation. Here, we discuss the benefits and challenges of IM-MSI data analysis in metabolomic applications. Finally, Pyxis, a novel, vendor-neutral IT solution for IM-MSI data analysis, is introduced and its capabilities demonstrated on mouse kidney tissue and THP-1 monocytes data.
    Keywords:  Chemometrics; Ion mobility; Mass spectrometry imaging; Metabolomics; Software and data analysis tools
    DOI:  https://doi.org/10.1007/s00216-025-06281-5
  2. Biomed Chromatogr. 2026 Jan;40(1): e70298
    Simultaneous Determination of Thioridazine and Its Metabolites by UHPLC-MS/MS With Application to a Pharmacokinetic Study in Rats.
    Kyung-Sun Moon, Jong-Min Song, Sung-Hoon Ahn.
      To develop an LC-MS/MS method for simultaneous quantification of thioridazine and its metabolites in rat plasma, samples were prepared by protein precipitation and filtration using thioridazine-d3 as an internal standard. Chromatographic separation was achieved on a reversed-phase C18 UPLC column with 0.1% formic acid in acetonitrile and 10-mM ammonium acetate in water at 0.7 mL/min. Quantification was performed using multiple reaction monitoring in positive ion mode with the following precursor-product ion transitions: m/z 371.1 → 126.1 (thioridazine), m/z 387.1 → 126.1 (mesoridazine), m/z 403.1 → 126.1 (thioridazine-2-sulfone), m/z 387.2 → 126.1 (thioridazine-5-sulfoxide), and 374.1 → 129.1 (thioridazine-d3). This method showed good linearity: 0.1-1000 ng/mL for thioridazine (r2 = 0.9980) and 0.5-1000 ng/mL for mesoridazine (r2 = 0.9981), thioridazine-2-sulfone (r2 = 0.9976), and thioridazine-5-sulfoxide (r2 = 0.9967). The accuracy of the LLOQ and QC samples for thioridazine and its metabolites was within 85%-115%, with intrabatch and interbatch precisions (CV%) below 15%. The average recovery ranged from 98% to 109%, and no significant matrix effect was observed, with values ranging from 93% to 110%. All analytes were stable under the conditions used in this study. This method was applied in a pharmacokinetic study following the intravenous administration of thioridazine to rats.
    Keywords:  LC–MS/MS; metabolites; pharmacokinetics; simultaneous determination; thioridazine; validation
    DOI:  https://doi.org/10.1002/bmc.70298
  3. J Biomol Tech. 2025 Sep 30. 36(3):
    A Taguchi Design of Experiments Approach for Untargeted Metabolomics Sample Preparation Optimization.
    Brianna M Garcia, Goncalo J Gouveia, Amanda O Shaver, Ricardo M Borges, I Jonathan Amster, Arthur S Edison, Franklin E Leach Iii.
      The field of metabolomics leverages advanced analytical techniques, such as nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS), to identify and quantify metabolites that are integral to biology. The scope of untargeted metabolomics methods is highly dependent on the protocols employed prior to analysis. These include homogenization and extraction processes, which directly influence the metabolites detected and, consequently, the biological interpretations drawn. Given the substantial variability introduced by different homogenization and extraction parameters, the optimization of these protocols for non-routine or novel sample matrices is essential, particularly in core facilities where a diverse range of matrices are expected to be analyzed. In response to this need, we demonstrate the utility of a Taguchi design of experiments (DOE) method for the systematic optimization of matrix-specific sample preparation parameters using the model organism Caenorhabditis elegans. This methodology was applied to optimize four critical factors: (1) extraction solvent, (2) solvent volume, (3) extraction duration, and (4) LC reconstitution solvent, during a sequential non-polar and polar metabolite extraction for LC-MS and NMR spectroscopy. Despite its infrequent use in metabolomics, the Taguchi DOE method offers a structured and efficient pathway for optimizing multiple sample preparation variables, enhancing throughput, reproducibility, and cost-effectiveness. This approach is particularly valuable for the metabolomics community, as it provides a scalable, adaptable framework applicable across various sample types and research objectives. This work serves as a demonstration of the methodology, underscoring its potential to enhance method development and optimization across diverse metabolomics applications.
    DOI:  https://doi.org/10.7171/3fc1f5fe.54585830
  4. Anal Chem. 2025 Dec 17.
    VirMolAnalyte: An AI-Driven In Silico Metabolite Annotation Tool.
    Guilin Hu, Jameel Hizam Alafifi, Minghua Qiu.
      Metabolites play a crucial role in sustaining biological activities and are also a significant source of new drug development. Nuclear magnetic resonance (NMR) spectroscopy is one of the most important tools for identifying the structures of the metabolites. However, the annotation of NMR spectra relies on costly experimental data. To address this challenge, we present a novel tool, VirMolAnalyte, which enables high-quality structural analysis of 13C DEPT NMR spectra without the reliance on experimental data. VirMolAnalyte employs a deep neural network to extract molecular fingerprints from 13C DEPT NMR spectra and utilizes a filter-evaluator strategy for multidimensional in silico database searching. When evaluated using DB6123, the filter-evaluator strategy achieved the highest Top 1 accuracy of 94.2%, outperforming the traditional chemical shift search method. In assessments conducted on the largest in silico metabolite database, Metabolites Multidimensional in silico Database, VirMolAnalyte demonstrated an impressive Top 1 accuracy of 90.0% and a Top 5 accuracy of 100.0%. VirMolAnalyte presents an innovative approach for the efficient analysis of metabolites using NMR data, providing significant advantages in new drug discovery and metabolomics research.
    DOI:  https://doi.org/10.1021/acs.analchem.5c03906
  5. Sichuan Da Xue Xue Bao Yi Xue Ban. 2025 Sep 20. 56(5): 1189-1196
    [Simultaneous Analysis of Microcystins, Cylindrospermopsin, Anatoxin, and Nodularin in Lake Water by Liquid Chromatography-Tandem Mass Spectrometry].
    Guanxiang Yuan, Qing Luo, Guihua Liu, Xiaoyun Qin, Honghe Liu, Zhaoying Lü, Jie Jiang.
       Objective: To establish a method for simultaneous determination of trace levels of microcystins, cylindrospermopsin, anatoxin, and nodularin in lake water based on liquid chromatography-tandem mass spectrometry (LC-MS/MS).
    Methods: After being adjusted to alkaline conditions and mixed with six internal standards, the water samples were enriched using dual HLB and ENVI-Carb cartridges. The eluates were then evaporated under nitrogen, reconstituted, and subjected to instrumental analysis. Both water and acetonitrile containing 0.1% formic acid were used as mobile phases. An ACQUITY UPLC® BEH C18 column (150 mm × 2.1 mm, 1.7 μm) was selected to separate the target cyanotoxins. Multiple reaction monitoring was applied for data acquisition, and quantification was accomplished using internal standard methods.
    Results: Within certain concentration ranges, all 14 cyanotoxins examined in the study showed good linearity, with all correlation coefficients greater than 0.998. When the water volume was 100 mL, the limits of detection and quantification for the 14 cyanotoxins were 0.1-0.9 ng/L and 0.3-2.9 ng/L, respectively, and spiked recoveries and relative standard deviations were 81.7%-132.9% and 1.2%-14.9%, respectively. In the 10 lake water samples analyzed, cylindrospermopsin, anatoxin-α, and multiple microcystins were detected.
    Conclusion: The method developed in the study has high-throughput capacity, as well as high sensitivity, accuracy, and reliability. The method can be applied in the simultaneous detection of microcystins, cylindrospermopsin, anatoxin, and nodularin in lake water.
    Keywords:  Cyanotoxins; Cylindrospermopsins; Lake water; Liquid chromatography-tandem mass spectrometry; Microcystins
    DOI:  https://doi.org/10.12182/20250960602
  6. Talanta. 2025 Dec 06. pii: S0039-9140(25)01717-5. [Epub ahead of print]300 129226
    Comprehensive preclinical pharmacokinetics and metabolite profiling of a novel caspase inhibitor F573.
    Yiping Gu, Xiaomin Ye, Shunchang Zhou, Fandian Zeng, Shan Wu, Qiongqiong Wang, Xueyan Miao, Ying Luo, Jianhong Wu.
      A robust and versatile bioanalytical method is essential for the preclinical development of the novel caspase inhibitor F573 for acute liver failure.This endeavor faces significant challenges, including the need for high sensitivity to monitor rapid systemic clearance, the ability to handle diverse and complex biological matrices (e.g., plasma, tissues, excreta), and overcoming potential interferences from high plasma protein binding (>89 %). To address these challenges, a sensitive, selective, and robust liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the quantification of F573 across these matrices, with additional capability for qualitative metabolite profiling. The method used a simple protein precipitation protocol optimized for high-throughput processing. It was rigorously validated per FDA guidelines, demonstrating a low limit of quantification (LLOQ of 2 ng mL-1 in 50 μL plasma), excellent precision (RSD <15 %), and accuracy. The method effectively addressed challenges from high plasma protein binding and matrix complexity. Its application enabled the first comprehensive characterization of F573's preclinical profile: it exhibited rapid absorption and elimination in rats and dogs, extensive tissue distribution, and limited blood-brain barrier penetration. Approximately 56 % of the administered dose was excreted unchanged, primarily via urinary and biliary routes. Furthermore, eight distinct metabolites were identified and profiled in rat samples. The developed LC-MS/MS method thus serves as a critical and reliable tool for the comprehensive preclinical pharmacokinetic evaluation of F573, underscoring its value in supporting the development of this promising therapeutic candidate.
    Keywords:  Bioanalytical method validation; F573; LC-MS/MS; Metabolite profiling; Pharmacokinetics; Tissue distribution
    DOI:  https://doi.org/10.1016/j.talanta.2025.129226
  7. J Chromatogr B Analyt Technol Biomed Life Sci. 2025 Dec 10. pii: S1570-0232(25)00447-7. [Epub ahead of print]1270 124893
    Assessment of the benefits of adding differential mobility spectrometry to LC-MS/MS workflows for challenging steroid measurements.
    Kayla Moehnke, Pragya Sharma, Jennifer Kemp, Anthony Maus.
      Accurate quantification of steroid hormones such as estrogens (estradiol, estrone) and glucocorticoids (cortisol, cortisone) is essential for diagnosing and monitoring endocrine disorders. However, their structural similarity and low physiological concentrations pose analytical challenges in clinical laboratories. This study evaluates the utility of differential mobility spectrometry (DMS) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) for improving the specificity and sensitivity of steroid measurements in serum (estrogens) and scalp hair (glucocorticoids) using a SelexION-equipped Sciex 6500+ mass spectrometer coupled to a high throughput Thermo Scientific TLX-2 LC system. DMS significantly reduced chromatographic interferences and enhanced signal-to-noise (S/N) ratios-up to 420 % for estradiol and 210 % for estrone. For cortisol and cortisone in hair, DMS also reduced interferences and increased S/N, as well as improving fragment ion agreement as evidenced by the reduction in fragment ion calculated concentration discrepancies exceeding ±20 % from 18 to 8 samples for cortisol and from 23 to 2 samples for cortisone. These findings support DMS as a complementary technique to LC-MS/MS, offering orthogonal separation and improved analytical performance for steroid hormone quantification in complex biological matrices.
    Keywords:  Differential mobility spectrometry; Ion mobility; LC-MS/MS; Steroid hormones
    DOI:  https://doi.org/10.1016/j.jchromb.2025.124893
  8. Anal Chem. 2025 Dec 17.
    In-Source Fragmentation Annotation in Sterol Mass Spectrometry Imaging.
    Iulia Sidorov, Nina Ogrinc, Lena Spieth, Michal Kopcil, Marieke Heijink, Hans Dalebout, Gesine Saher, Stefan A Berghoff, Gary Siuzdak, Martin Giera.
      Spatial biology has emerged as a pivotal area in many life science fields, with mass spectrometry imaging (MSI) becoming a cornerstone for molecular imaging. Among recent advancements to increase sensitivity, MALDI-2 technology has significantly expanded the molecular space accessible to MSI, increasing the ion yields of neutral metabolites, such as sterols. Sterols have recently taken center stage in numerous (patho-) physiological processes, including neurodegenerative diseases that have attracted significant scientific interest. However, in-source fragmentation (ISF) poses a substantial challenge for accurate biological interpretation of mass spectrometric data. In this study, we observed and investigated the ISF of cholesterol during MSI under MALDI and MALDI-2 conditions. Using a murine intervention model, we demonstrate how ISF can compromise the accuracy of biological interpretations, potentially leading to significant misinterpretations. Our study underscores the critical need to address ISF to ensure accurate molecular annotation, particularly through tandem mass spectrometry of in-source fragments. This is especially important when using MALDI-2 techniques. Furthermore, we introduce a high-resolution (5 μm) MSI technique, enabling the precise spatial analysis of cholesterol distribution.
    DOI:  https://doi.org/10.1021/acs.analchem.5c05199
  9. Clin Chem Lab Med. 2025 Dec 16.
    Quantitative analysis of phylloquinone (vitamin K1) and menaquinone (vitamin K2) in serum of Russians by liquid chromatography-tandem mass spectrometry.
    Mikhail Vokuev, Anastasia Frolova, Stepan Makarkin, Daria Prosuntsova, Timur Baygildiev, Lidia Nefedova, Oleg Klychnikov, Igor Rodin.
       OBJECTIVES: Vitamin K homologues are essential to human health, and their concentrations in biological samples serve as valuable diagnostic biomarkers. This study was aimed to develop a method for determining vitamins K1 (phylloquinone, VK1) and K2 (menaquinone, MK-4) in human serum. The proposed method was validated and applied to the serum of a cohort of 20 Russian individuals.
    METHODS: High-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS) was used to analyse the content of VK1 and MK-4 in serum. Atmospheric pressure chemical ionisation (APCI) in negative mode was applied to ionise VK1 and MK-4. Protein precipitation and solid-phase extraction (SPE) on polystyrene-divinylbenzene resin were combined to isolate and preconcentrate the analytes from serum.
    RESULTS: The HPLC-MSMS method was developed and validated for the determination of vitamins VK1 and MK-4 in human serum. The method demonstrated a lower limit of quantification (LLOQ) of 0.05 μg/L, with more than 71 % recoveries and precision within 17 %. To demonstrate the applicability of the method to real samples, serum from 20 healthy adults was analyzed. VK1 was detected in four individuals (0.094-0.96 μg/L), whereas MK-4 concentrations were below 0.22 μg/L in all cases.
    CONCLUSIONS: The validated HPLC-MS/MS workflow provides a reliable and sensitive approach for the quantification of VK1 and MK-4 in minimal serum volumes. The method demonstrates robustness, reproducibility, and suitability for large-scale analytical applications. The proposed LC-MS/MS protocol successfully applied to native human serum samples, illustrating its applicability for future clinical and biochemical studies involving vitamin K.
    Keywords:  liquid chromatography; menaquinone; phylloquinone; serum levels; tandem mass spectrometry; vitamins
    DOI:  https://doi.org/10.1515/cclm-2025-0719
  10. Clin Chem Lab Med. 2025 Dec 18.
    Development and validation of a candidate reference measurement procedure for free triiodothyronine and free thyroxine in human serum using equilibrium dialysis isotope-dilution liquid chromatography-tandem mass spectrometry.
    Min Zhan, Qiaoxuan Zhang, Zijia Ma, Liqiao Han, Jun Yan, Guangya Zheng, Wenxi Zhou, Weiyan Zhou, Xianzhang Huang.
       OBJECTIVES: Free triiodothyronine (FT3) and free thyroxine (FT4) are important diagnostic markers for assessing thyroid function. However, their accurate quantification remains challenging due to low serum concentrations. Significant variability exists among current assay methods for measuring FT3 and FT4. This study aims to establish a candidate Reference Measurement Procedure (cRMP) for simultaneous quantification of serum FT3 and FT4 based on isotope-dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) technology.
    METHODS: A convenient and reusable equilibrium dialysis (ED) device was utilized to separate free thyroid hormones from their protein-bound counterparts in serum. Key dialysis parameters, including temperature, pH, membrane type, and duration, were optimized to ensure consistent and reliable performance. The dialysate containing FT3 and FT4 was directly quantified by ID-LC-MS/MS. The method underwent systematic validation, comparative analysis with existing assays, and a comprehensive uncertainty assessment.
    RESULTS: The developed cRMP demonstrated limits of quantification (LoQ) of 1.54 pmol/L for FT3 and 3.22 pmol/L for FT4, and with an imprecision of less than 3 %. No interference from endogenous analogs was observed, and the method showed good consistency in interlaboratory comparison. In contrast, chemiluminescent immunoassay results exhibited poor agreement with and the cRMP.
    CONCLUSIONS: This study developed a highly precise, accurate, specific, and sensitive ID-LC-MS/MS-based cRMP for the simultaneous measurement of FT3 and FT4 in human serum. This method provides a reliable tool for standardizing routine thyroid function tests.
    Keywords:  ID-LC-MS/MS; candidate reference measurement procedure; equilibrium dialysis; free thyroxine; free triiodothyronine; standardization
    DOI:  https://doi.org/10.1515/cclm-2025-0874
  11. Crit Rev Anal Chem. 2025 Dec 18. 1-17
    An Analytical Perspective on Liquid Chromatography-Mass Spectrometry Methods for the Analysis of Bile Acids in Human Blood Samples.
    Monika Sostaric, Hayley Abbiss, Armaghan Shafaei.
      Bile acids (BA) are traditionally recognized as detergents that facilitate lipid and glucose digestion and homeostasis. More recently, they have emerged as signaling molecules with the ability to influence metabolic processes via the gut-brain axis. BA are implicated in a wide range of diseases and conditions, including gastrointestinal, hepatobiliary, metabolic, cardiovascular, and neurological disorders. Accurate quantification of total bile acids (TBA) and individual BA species is essential for understanding their roles in health and disease. Liquid chromatography coupled with mass spectrometry (LC-MS) offers the sensitivity and selectivity required to detect these metabolites at trace levels in human blood samples. This systematic review critically examines validated LC-MS methodologies for BA analysis in human blood, focusing on studies published between January 2010 and April 2024. It highlights experimental designs, validation criteria, and methodological differences, aiming to inform the development of standardized analytical protocols. By addressing current gaps and emphasizing comprehensive analytical validation, this review seeks to enhance the reliability of BA quantification and support future biomarker discovery and clinical applications.
    Keywords:  Bile acids; LC-MS; human blood; liquid chromatography; mass spectrometry
    DOI:  https://doi.org/10.1080/10408347.2025.2599298
  12. Anal Bioanal Chem. 2025 Dec 15.
    Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites.
    Nikita Denisov, Fabian Springer, Amber Brauer-Nikonow, George Maftei, Georg Zeller, Denise Medeiros Selegato, Michael Zimmermann.
      The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer. Here, we developed a gas chromatography-coupled tandem mass spectrometry (GC-MS/MS) method for the quantification of 120 volatile and semi-volatile compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives. The method is based on multiple-reaction-monitoring (MRM) of each analyte and their respective isotopically labeled internal standard, enabling absolute metabolite quantification between 0.45 pmol and 1 nmol. Applying the method to different tissue samples from germfree and conventionally colonized mice, we illustrate the ability to quantify microbiota-produced metabolites in different sample matrices-plasma, liver, feces, and intestinal content-and at different concentrations. Lastly, we demonstrate that this protocol is capable of quantifying microbiota-derived metabolites in stool samples stored in DNA stabilization buffers that are typically used in sequencing-based microbiome studies. Altogether, the developed GC-MS/MS method adds a valuable analytical tool to quantify microbiota-host metabolic interactions.
    Keywords:  Bacterial metabolites; DNA stabilization buffers; GC-MS/MS; Gut microbiota
    DOI:  https://doi.org/10.1007/s00216-025-06256-6
  13. J Pharm Anal. 2025 Nov;15(11): 101289
    Recent advances in mass spectrometry-based bioanalytical methods for endogenous biomarkers analysis in transporter-mediated drug-drug interactions.
    Dang-Khoa Vo, Han-Joo Maeng.
      Drug-drug interactions (DDI) are a critical concern in drug development and clinical practice. A new molecular entity often requires numerous clinical DDI studies to assess potential risks in humans, which involves significant time, cost, and risk to healthy study participants. Consequently, there is growing interest in innovative techniques to improve the prediction of transporter-mediated DDI. Researchers in this field have focused on identifying endogenous molecules as biomarkers of transporter function. The development of biomarkers is notably more complex than that of exogenous drugs. Owing to their inherent selectivity, sensitivity, and ability to provide absolute quantification, liquid chromatography-mass spectrometry (LC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) are increasingly being employed for the quantitative investigation of new biomarkers. This review article presents recently developed bioanalytical approaches using LC-MS/MS for putative transporter biomarkers identified to date. Additionally, we summarize the published baseline endogenous levels of these potential biomarkers in a biological matrix to suggest a set of reference values for future research, thereby minimizing errors in biomarker-related data analyses or calculations.
    Keywords:  Biomarkers; Drug development; Drug-drug interactions; Mass spectrometry; Pharmacokinetics; Transporters
    DOI:  https://doi.org/10.1016/j.jpha.2025.101289
  14. J Sep Sci. 2025 Dec;48(12): e70334
    Overcoming the Challenge of Confident Identification Among Two Related Groups of 17-Methyl Steroids by GC-MS.
    Jakob Steff, Xavier de la Torre, Francesco Botrè, Maria Kristina Parr.
      Tetrahydromethyltestosterone (THMT) and 20-hydroxymethyl-18-nortetrahydromethyltestosterone (20OHnorTHMT) are metabolites of the anabolic androgenic steroids methyltestosterone and metandienone. Both molecular structures are used as markers in anti-doping analysis. There are eight reasonable diastereomeric structures of each group relevant for metabolic purposes. Highly sophisticated mass spectrometers fail to confidently differentiate these closely related, yet non-isomeric and non-isobaric groups of molecules. Due to the low abundance of the molecular ion, high-resolution mass spectrometry provides shared fragment ions that challenge identification by extracted ion chromatograms out of full scan mode acquisitions. Further on, tandem mass spectrometry uses partly the same ion transitions for both groups of targeted analytes. Thus, a reliable chromatographic separation is absolutely necessary. Therefore, a gas chromatographic method using a DB-5 ms capillary column (30 m, 0.25 mm, and 0.25 µm) was developed. Hence, discrimination between the two groups was enabled, and a confident structural assignment among the eight diastereomers was achieved. This case study contributes to a higher quality of anti-doping analysis, but even further raises awareness of the importance of chromatographic separation in cases of insufficient mass spectrometric discrimination.
    Keywords:  anabolic androgenic steroids; anti‐doping analysis; chromatographic separation; mass spectrometry; method development
    DOI:  https://doi.org/10.1002/jssc.70334
  15. J Anal Toxicol. 2025 Dec 19. pii: bkaf107. [Epub ahead of print]
    Analysis of propranolol and its metabolites in postmortem human solid tissues and body fluids: LC-MS/MS approach with the standard addition method applied to a forensic case.
    Mengchao Wang, Xiaoyu Zhou, Xiaolong Zhang, Yuxuan Chen, Jiajun Sun, Yaqin Sun, Jinlei Liu, Jie Gu, Amin Wurita, Hasegawa Koutaro.
       PURPOSE: This study aimed to develop a highly sensitive and specific liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the simultaneous determination of propranolol and its metabolites in human biological samples. By analyzing their presence in urine, postmortem biological fluids, and various solid tissues, the study could be of reliable forensic toxicological use for investigations in propranolol poisoning cases. In this study, the Standard Addition Method (SAM) was used for quantification, and its validation was mixed with one of the analyte's concentrations.
    METHODS: A 0.1 mL aliquot of each body fluid sample or 0.1 g each of homogenized solid tissue was mixed with one of the analyte concentration standards, extracted with methanol, spiked with an internal standard (IS) using the SAM, and purified using magnesium sulfate and sodium sulfate. Following centrifugation and filtration, samples were analyzed via LC-MS/MS. Urine samples underwent enzymatic hydrolysis with sulfatase and β-glucuronidase to measure conjugated metabolite forms prior to analysis.
    RESULTS: Phase I metabolites (propranolol, 4-hydroxypropranolol, propranolol glycol, N-desisopropylpropranolol, 1-naphthylenyloxyacetic acid, and 1-naphthol) and phase II metabolites (sulfate and glucuronide conjugates) were identified in urine. Among postmortem samples, propranolol was highest in the bile, followed by the lung tissue. Naphthoxylactic acid could be consistently detected in all samples except for the brain, suggesting its potential as a good biomarker for propranolol exposure.
    CONCLUSION: A validated LC-MS/MS method for determining propranolol and its metabolites in forensic samples was established, and it could also be applied to the authentic human samples obtained from a propranolol poisoning case. The findings could offer substantial and reliable support for investigating propranolol-related fatalities and contribute to the comprehensive understanding of the metabolism of propranolol in the human body.
    Keywords:  Human biological samples; LC-MS/MS; Propranolol; metabolites
    DOI:  https://doi.org/10.1093/jat/bkaf107
  16. Anal Chem. 2025 Dec 17.
    Epoxidation-Enhanced Charge-Switch Derivatization for Rapid Profiling of Monounsaturated Fatty Acid Isomers.
    Sarah E Hancock, Linda Garthwaite, Laura L Y Choong, Iliya Dragutinovic, Jonathan C Morris, Nigel Turner.
      Structural isomerism in monounsaturated fatty acids (MUFAs) presents a persistent challenge in lipidomics due to limited chromatographic resolution and indistinguishable mass spectral profiles. Moreover, many methods that overcome these limitations require specialized instruments or additional apparatus that are typically not available for those using standard lipidomics core facilities. We report a streamlined LC-MS/MS method that integrates N-(4-aminomethylphenyl)pyridinium (AMP)-based charge-switch derivatization with meta-chloroperoxybenzoic acid (mCPBA) epoxidation to enable rapid and sensitive profiling of MUFA double bond positional isomers. Charge-switching enables enhanced detection of fatty acids, while epoxidation improves chromatographic resolution and produces diagnostic fragmentation patterns upon collision-induced dissociation (CID), enabling precise localization of double bond positions. The optimized workflow achieves baseline separation of 16:1, 18:1, and 20:1 MUFA isomers within a 20 min gradient, with reproducible retention times and consistent epoxide yields. The method also supports partial resolution of polyunsaturated fatty acids (PUFA) and cis/trans isomers. Application to prostate cancer cell lines revealed distinct MUFA isomer profiles associated with aberrant fatty acid desaturase 2 (FADS2) activity, including elevated n-10 and n-12 isomers in tumorigenic lines. These results align with prior studies using other isomer-resolving techniques, validating the method's analytical performance. This accessible and robust strategy expands the toolkit for lipidomics research, providing a method that is compatible with conventional LC-MS/MS workflows, positioning it as a practical solution for high-resolution isomer analysis in complex biological samples.
    DOI:  https://doi.org/10.1021/acs.analchem.5c06149
  17. Sichuan Da Xue Xue Bao Yi Xue Ban. 2025 Sep 20. 56(5): 1226-1234
    [High-Throughput Determination of Endogenous Peptides in Urine Using Electromembrane Extraction Combined With Liquid Chromatography-Tandem Mass Spectrometry].
    Yong Tang, Junling He, Chiliang Lin, Shaoyun Peng, Haimin Zou, Chen Zhou.
       Objective: To develop a precise method for analyzing urinary peptides based on electromembrane extraction (EME) combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and to evaluate its potential applicability in tumor biomarker screening.
    Methods: A total of 15 disease-associated peptides were selected as the target analytes. A supported liquid membrane (SLM) composed of n-octanol containing 5% di (2-ethylhexyl) phosphate was employed, with the donor phase being a 1∶1 mixture of urine and 100 mmol/L formic acid and urine, and the acceptor phase being 20 mmol/L formic acid containing 50% dimethyl sulfoxide (DMSO). After EME at 40 V for 15 min, the acceptor phase solution was analyzed by LC-MS/MS. Subsequently, the method, EME combined with LC-MS/MS (EME-LC-MS/MS), was preliminarily validated utilizing urine samples from 12 healthy controls and 7 patients with urinary system tumors.
    Results: All 15 peptides exhibited excellent linearity in the range of 0.1-100.0 ng/mL (r ≥ 0.995), with the limits of detection (LODs) being 0.01-0.50 ng/mL and the limits of quantification (LOQs) being 0.03-1.50 ng/mL. The spiked recoveries ranged from 21.0% to 71.2%, with relative standard deviations (RSDs) of 0.8%-20.0% (n = 3). Small-sample analysis of clinical specimens revealed that the concentration of bradykinin 1-5 in the urine were significantly higher in tumor patients (median: 0.65 ng/mL) than that in healthy controls (median: 0.37 ng/mL) (P < 0.05), suggesting its potential as a specific biomarker for urinary system tumors.
    Conclusion: The EME-LC-MS/MS method established in the study features simplicity, high efficiency, and high sensitivity, enabling precise determination of trace-level peptides in urine samples. Moreover, this approach provides a reliable methodological basis for disease biomarker screening and promotes the clinical application of electromembrane extraction.
    Keywords:  Electromembrane extraction; Microextraction; Peptides; Tumor biomarkers; Urine
    DOI:  https://doi.org/10.12182/20250960502
  18. medRxiv. 2025 Dec 11. pii: 2025.12.10.25341983. [Epub ahead of print]
    Longitudinal, intra-individual stability of untargeted plasma and cerebrospinal fluid metabolites.
    Briana Rocha, Erin Jonaitis, Alana Hamwi, Corinne D Engelman.
       Background/Objectives: Longitudinal metabolomics analysis offers valuable insight into how metabolic pathways change according to age and health status. However, metabolite levels can fluctuate due to biological factors (ex. age, diet, health-status) and technical factors (ex. sample handling, storage times, instrument performance), with some metabolites exhibiting greater sensitivity to these sources of variability than others. This study aimed to characterize the longitudinal and technical stability of untargeted plasma and cerebrospinal fluid (CSF) metabolites, and to identify a subset that remains reliable over the extended time scales required for epidemiological research.
    Methods: Untargeted ultra-high-performance liquid chromatography-mass spectrometry (LC-MS) metabolomic profiles were available from multiple visits in the Wisconsin Registry for Alzheimer's Prevention (WRAP) and Wisconsin Alzheimer's Disease Research Center (ADRC) studies. For this analysis, we constructed a subset of generally healthy participants with samples drawn at four time points (∼2.5 years apart): two visits analyzed in 2017 and two visits analyzed in 2023, corresponding to two distinct analytical waves. We computed Rothery's intraclass correlation coefficients (ICCs) to quantify intrawave and inter-wave stability, evaluated pooled quality-control (QC) variation, classified metabolite stability by established thresh-olds, and developed a composite score integrating longitudinal stability and susceptibility to technical variance.
    Results: Across all metabolites, median stability was classified as fair (Rothery's ρ >0.40 to ≤0.75) for both plasma and CSF. Although analytical batches were bridged using pooled QC samples, inter-wave stability was significantly lower than intra-wave stability, reflecting increased technical variability across waves. Using the composite score, we identified subsets of metabolites with excellent stability and low susceptibility to batch effects in plasma and CSF. Stability patterns varied across biochemical super pathways.
    Conclusions: This work highlights metabolites suitable for long-term epidemiological studies and informs experimental design and analytical strategies for combining data across cohorts and analytical batches.
    DOI:  https://doi.org/10.64898/2025.12.10.25341983
  19. Sichuan Da Xue Xue Bao Yi Xue Ban. 2025 Sep 20. 56(5): 1215-1225
    [Determination of 18 Perfluorinated Compounds in Tea Leaves by a Quick, Easy, Cheap, Effective, Rugged, and Safe Method Combined With Ultra-High Performance Liquid Chromatography-Tandem Mass Spectrometry].
    Weiyang Sun, Yujing Chuai, Xiaotao Zhou, Tianai Zhang, Li Yong, Lin Ren, Xinyue Luo, Xiaoli Zou.
       Objective: To establish an analytical method for the simultaneous determination of 18 perfluoroalkyl compounds (PFCs) in tea leaves using a quick, easy, cheap, effective, rugged, and safe (QuEChERS) method for sample pretreatment combined with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS).
    Methods: The target analytes-18 PFCs-included 13 carboxylic acid PFCs (perfluorobutanoic acid [PFBA], perfluoropentanoic acid [PFPeA], perfluorohexanoic acid [PFHxA], perfluoroheptanoic acid [PFHpA], perfluorooctanoic acid [PFOA], perfluorononanoic acid [PFNA], perfluorodecanoic acid [PFDA], perfluoroundecanoic acid [PFUdA], perfluorododecanoic acid [PFTrDA], perfluorotridecanoic acid [PFTeDA], perfluorotetradecanoic acid [PFHxDA], perfluorohexadecanoic acid [PFHpS], and perfluorooctadecanoic acid [PFODA]) and 5 sulfonic acid PFCs (perfluorobutanesulfonic acid [PFBS], perfluorohexanesulfonic acid [PFHxS], perfluoroheptanesulfonic acid [PFHpS], perfluorooctanesulfonic acid [PFOS], and perfluorodecanesulfonic acid [PFDS]). The QuEChERS pretreatment parameters were systematically optimized using the response surface methodology. The tea leave samples were extracted with an 80% acetonitrile solution and subsequently purified by adding a mixed absorbent consisting of 20 mg N-propyl-ethylenediamine (PSA), 210 mg graphitized carbon black GCB), and 60 mg octadecylsilane (C18). The supernatant was concentrated by nitrogen blowing and subsequently re-dissolved in 50% methanol-2 mmol/L ammonium acetate solution. The re-dissolved solution was injected into the UHPLC-MS/MS for analysis. The target analytes were separated on an ACQUITY UPLC BEH C18 column (2.1 mm × 50 mm, 1.7 µm). The mobile phases consisted of methanol (phase A) and 2 mmol/L aqueous ammonium acetate (phase B), with a gradient elution procedure. The total running time was 18 min. The mass spectrometry analysis was conducted using an electrospray ionization source in negative ionization mode and multi-reaction monitoring (MRM), with quantification performed using the internal standard curve method. The greenness of the analytical method was assessed using Analytical GREEnness calculator (AGREE) and the Analytical Eco-Scale method (AES).
    Results: Under the optimized conditions, the limits of detection (LODs) and limits of quantification (LOQs) of the method were 0.0057-1.23 ng/g and 0.019-4.09 ng/g, respectively. The average recoveries of most target compounds were 71.1%-117.9%, with relative standard deviations (RSDs) below 15%. The AGREE index of the method was 0.49, and the AES score was 76. At least one PFC was detected in each of the 132 tea leave samples, and the detection rate of carboxylic acid PFC was higher than that of sulfonic acid PFC. The highest detection rates were observed for PFBA at 97.74%, PFHpA at 93.23%, and PFOA at 92.24%. In contrast, PFHpS, PFUdA, PFDoA, PFHxDA, and PFODA were not detected in the samples.
    Conclusion: The proposed method has the advantages of simplicity, rapidity and sensitivity, and is suitable for the analysis of PFCs in tea leaves. The method has high greenness with minimal impact on the operator and the environment. The widespread presence of PFC contamination in tea leaves available in the market warrants strengthened monitoring and regulatory control.
    Keywords:  Perfluorinated compounds; Quick, Easy, Cheap, Effective, Rugged, and Safe （QuECHERS）; Response surface method; Tea; Ultra-performance liquid chromatography-tandem mass spectrometry
    DOI:  https://doi.org/10.12182/20250960603
  20. Commun Chem. 2025 Dec 18. 8(1): 398
    mzLearn as a data-driven LC/MS signal detection algorithm that enables pre-trained generative models for untargeted metabolomics.
    Leila Pirhaji, Jonah Eaton, Adarsh K Jeewajee, Min Zhang, Matthew Morris, Maria Karasarides.
      Metabolite alterations are linked to diseases, yet large-scale untargeted metabolomics remains constrained by challenges in signal detection and integration of diverse datasets for developing pre-trained generative models. Here, we introduce mzLearn, a data-driven MS¹ signal-detection and alignment method that runs from mzML files without user-set parameters. Across 15 public datasets, mzLearn detects 11,442 signals on average vs 7,100 (XCMS) and 4,655 (ASARI), with higher TP (89.0% vs 77.4% vs 49.6%) and lower FP (12.5% vs 17.3% vs 18.8%), while correcting instrument drifts across large cohorts without experimental QC samples. mzLearn detected 2,736 robust metabolite signals from 22 public studies (20,548 blood samples), enabling the development of pre-trained variational autoencoder for untargeted metabolomics. Learned metabolite representations reflected demographic data and when fine-tuned on unseen renal cell carcinoma data, improved risk stratification and overall survival predictions, while feature-importance analysis (SHAP) highlighted biologically plausible lipid and carnitine signals. By producing a consistent, high-quality MS¹ feature matrix at scale, mzLearn paves the way for developing pre-trained foundation models for untargeted metabolomics.
    DOI:  https://doi.org/10.1038/s42004-025-01791-w
  21. Forensic Toxicol. 2025 Dec 15.
    Quantitative determination of suvorexant, lemborexant, and daridorexant in human plasma using a MonoTip C18 and gas chromatography-mass spectrometry.
    Koichi Aoyama, Chika Hasegawa, Masaya Fujishiro, Maiko Kusano, Takeshi Kumazawa, Akihiro Nakauchi, Motofumi Miura, Mitsuru Honda, Takaaki Matsuyama, Kunihiko Kurosaki.
       PURPOSE: Orexin receptor antagonists (ORAs) are a novel class of medications used in the treatment of insomnia. With increasing restrictions on benzodiazepine prescriptions, a rise in ORA overdose is expected. To enable the prediction of clinical severity and formulation of appropriate treatment strategies, we developed a rapid analytical method for detecting ORAs in plasma samples using a Monolithic solid-phase extraction (SPE) and gas chromatography-mass spectrometry (GC-MS).
    METHOD: Extraction was performed using MonoTip C18. All steps from pretreatment to elution were conducted using centrifugation. Quantification was carried out using GC-MS with temperature-programmed analysis by positive ion electron ionization, using suvorexant-d6 as the internal standard. The method was applied to plasma samples from actual ORA overdose cases to evaluate its practical applicability.
    RESULT: The calibration curves demonstrated excellent linearity over the range of 10-2,000 ng/mL, with correlation coefficients of at least 0.9999. Reproducibility showed a coefficient of variation (CV) between 0.6% and 6.9%, and recovery rates were over 83%. ORA concentrations in overdose patient samples were successfully quantified using this method.
    CONCLUSION: MonoTip C18 utilizes a reduced amount of solvent, thereby eliminating the need for evaporation-to-dryness steps. As a result, the entire procedure, encompassing SPE to GC-MS detection, can be completed within 40 min. This single protocol is applicable to all ORAs currently available in Japan and is suitable for both clinical and forensic toxicological applications.
    Keywords:  Gas chromatography; Mass spectrometry; MonoTip C18; Orexin receptor antagonist; Solid-phase extraction
    DOI:  https://doi.org/10.1007/s11419-025-00745-0
  22. Sci Rep. 2025 Dec 19. 15(1): 44180
    Simultaneous determination of vitamin B12 and cobalt (II) in infant milk power using liquid chromatography-inductively coupled plasma mass spectrometry.
    Jun Tang, Xiaofeng Yu, Lijun Zhao, Chenyang Zheng, Ying Tan, Heng Wang.
      A new method was developed for simultaneous determination of cobalamin compounds [cyanocobalamin (CN-Cbl), hydroxocobalamin (OH-Cbl), 5'-deoxyadenosylcobalamin (Ado-Cbl) and methylcobalamin (Me-Cbl)] and inorganic cobalt ions [Co(II)] in infant milk powder by liquid chromatography-inductively coupled plasma mass spectrometry (LC-ICP-MS). The samples were enzymatic hydrolyzed by pepsin (porcine source) and the analytes extracted in the hydrolysate were measured directly by LC-ICP-MS after filtration. The chromatographic separation was performed on a Phenomenex Luna 5 μm C18 (250 mm × 4.6 mm) column. The mobile phase was consist of 1.6 mM ethylenediaminetetraacetic acid disodium salt (EDTA•2Na) and 0.4 mM potassium dihydrogen phosphate in 60% (v/v) methanol-water (pH = 6.0) (mobile phase A) and ultrapure water (mobile phase B). After LC separation with gradient elution, Co(II), OH-Cbl, CN-Cbl, Ado-Cbl, and Me-Cbl were measured as 59Co by ICP-MS. The method detection limit of Co(II), OH-Cbl, CN-Cbl, Ado-Cbl, and Me-Cbl were 0.144 µg/kg, 0.197 µg/kg, 0.267 µg/kg, 0.209 µg/kg and 0.278 µg/kg, respectively. At three spiked levels (1.0, 10.0, 50.0 µg/kg), the average recoveries (%) of Co(II), OH-Cbl, CN-Cbl, Ado-Cbl, and Me-Cbl ranged from 70.4 to 79.6, 74.5 to 77.4, 91.0 to 93.1, 83.0 to 83.8, and 84.3 to 90.2, respectively. The relative standard deviations (RSD, %) of Co(II), OH-Cbl, CN-Cbl, Ado-Cbl, and Me-Cbl ranged from 0.50 to 2.57, 0.70 to 6.29, 0.80 to 2.37, 1.33 to 2.50, and 1.16 to 2.40, respectively. These results indicating that the method had a good accuracy and precision. The preparation of sample was simple and less time consuming since it avoiding solid phase extraction and follow steps.
    Keywords:  Cobalamins; Infant milk powder; LC-ICP-MS; Vitamin B12
    DOI:  https://doi.org/10.1038/s41598-025-27805-0
  23. Bioanalysis. 2025 Dec 16. 1-8
    Bioanalytical method development for polmacoxib in rat plasma using LC-MS/MS and Its preclinical pharmacokinetic evaluation.
    Aniket Sohani, Shubham Debaje, Kajal Guleria, Sahil Sankulkar, Khushi Gupta, B Mohan Reddy Bandi, Nitin M Mehetre, Abhay T Sangamwar.
       AIM: To develop and validate a rapid, sensitive, and selective LC - MS/MS method for quantifying polmacoxib (POL) in rat plasma and integrating for preclinical pharmacokinetic evaluation.
    MATERIALS AND METHODS: POL was quantified using LC - MS/MS on a Varian C8 column with an isocratic mobile phase of methanol and 2 mM ammonium acetate (90:10, v/v; 0.4 mL/min) with run time of 6 min. Detection employed negative ion electrospray and MRM (m/z 360 → 296 for POL; m/z 313 → 257 for rofecoxib as IS). The method was validated as per USFDA guidelines. Male Sprague - Dawley rats received a single oral dose of 10 mg/kg POL, and plasma samples were collected up to 72 h.
    RESULTS: The method showed linearity (1.56-800 ng/mL, r2  = 0.9994), LLOQ 1.56 ng/mL, and acceptable accuracy, precision, recovery, and matrix effects. Pharmacokinetics: Cmax 643 ± 32 ng/mL, Tmax 4 h, T1/2 10.4 ± 0.8 h, AUC0-∞ 5326 ± 106 ng*h/mL.
    CONCLUSIONS: The validated assay is robust, sensitive, and suitable for pharmacokinetic, bioequivalence, and drug - drug interaction studies of POL.
    Keywords:  LC–MS/MS; Polmacoxib; bioequivalence; chromatography; pharmacokinetics
    DOI:  https://doi.org/10.1080/17576180.2025.2601870
  24. Biomed Chromatogr. 2026 Jan;40(1): e70326
    LC-MS/MS and GC-MS Analysis-Based Novel Bioactive Compounds From Endophyte Acremonium sclerotigenum CBS 124.42 Isolated From Stevia rebaudiana (Bertoni) Bertoni.
    Nishant, Sheela Chandra.
      Endophytes are microorganisms that reside inside the living tissues of leaves and possess antimicrobial, antioxidant, anticancer and anti-inflammatory activity etc. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) represents a powerful analytical platform for comprehensive metabolomic profiling of endophytic fungi, offering superior sensitivity, selectivity and structural elucidation capabilities compared to conventional methods. This study employed LC-MS/MS and GC-MS analyses to characterise bioactive compounds from the methanolic extract of endophytic fungus Acremonium sclerotigenum CBS 124.42 isolated from Stevia rebaudiana leaves. LC-MS/MS analysis identified nine major bioactive compounds, including flavonoid glycosides (928.4 m/z), rutin derivatives (1454.7 m/z), cyclic depsipeptides (1445.4 m/z), cyanidin-3-O-rutinoside (595.3 m/z), macrolactams (1394.2 m/z), proanthocyanins (1232.8 m/z), oligomeric imperatorin (676.8 m/z) and cyanidin-3-O-glucoside (1232.8 m/z). Stevioside was detected at 9.02 min with characteristic fragments at 317.9 m/z. GC-MS analysis revealed 18 distinct compounds, with benzene (azidomethyl) being most abundant (100% relative area), followed by hydrazine carbothioamide (71.3%) and benzyl(1,2,3-thiadiazol-4-yl) carbamate (43.22%). Significantly, this study reports the first identification of hydrazine carbothioamide and benzyl(1,2,3-thiadiazol-4-yl) carbamate from natural sources, compounds previously known only from chemical synthesis. These compounds demonstrated significant bioactivities including antioxidant (IC50 = 28.1 ± 6.96 mg/g), antimicrobial (zone of inhibition: 10.3-23.6 mm) and anticancer properties, establishing A. sclerotigenum CBS 124.42 as a novel source of therapeutically relevant secondary metabolites.
    Keywords:  GC–MS; LC–MS; endophyte; glycoside; stevioside
    DOI:  https://doi.org/10.1002/bmc.70326
  25. Anal Chem. 2025 Dec 18.
    Coupling Liquid Chromatography to Orbitrap Isotope Ratio Mass Spectrometry: Overcoming Isotope Effects of Chromatography and Amount-Dependency by Peak Homogenization.
    Aoife Canavan, Leonhard Prechtl, Habib Al-Ghoul, Nils Kuhlbusch, Andrea M Erhardt, Martin Elsner.
      Electrospray ionization Orbitrap mass spectrometry (ESI-Orbitrap-MS) has recently proven to be a powerful tool for compound- and position-specific stable isotope analysis, targeting isotopologues of multiple elements (H, C, N, O, S) in polar analytes. However, studies have so far mainly focused on pure analyte solutions via direct infusion. Here, we present the online coupling of liquid chromatography (LC) to ESI-Orbitrap-MS for stable isotope analysis of sulfamethoxazole (SMX), a synthetic antimicrobial, used as a model compound. Our study explored the fidelity of isotope values with two strategies for capturing and broadening chromatographic peaks after LC. When capturing the target analyte in a capillary (0.7 mm inner diameter), peak shape was retained, resulting in systematic deviations in isotope values caused by isotope effects from chromatography of up to 70‰ and amount-dependency of up to 65‰. A dynamic mixing chamber was used to homogenize the target analyte upon elution, removing these deviations and resulting in stable carbon, nitrogen, and sulfur isotopologue ratios in various fragments of sulfamethoxazole across the chromatographic peak. Comparison with data from conventional magnetic sector isotope ratio mass spectrometry successfully calibrated the setup for carbon and sulfur isotope ratio analysis. This resulted in a precision for δ13C within the isoxazole moiety from SMX of 1.5‰ (95% confidence intervals CIs derived from uncertainties of sample (n = 4) and reference (n = 5)), and for δ34S in the SO2 fragment of 0.9‰ (95% CI, derived again from uncertainties of sample (n = 4) and reference (n = 5)). This work paves the way for the online coupling of LC to ESI-Orbitrap-MS in future compound- and position-specific stable isotope analyses across various research fields.
    DOI:  https://doi.org/10.1021/acs.analchem.5c05530
  26. PLoS Comput Biol. 2025 Dec 15. 21(12): e1013095
    LCMSpector: A simple open-source viewer for targeted hyphenated mass spectrometry analysis.
    Mateusz Fido, Etienne Hoesli, Elisa Cappio Barazzone, Renato Zenobi, Emma Slack.
      The ubiquitousness of hyphenated mass spectrometry techniques across life sciences has made researchers around the world aware of their analytical power. However, the analysis of multidimensional high-complexity mass spectrometry data remains virtually impossible for non-specialists. LCMSpector is a standalone graphical user interface application for straightforward analysis of targeted mass spectrometry data, distributed under the MIT license and available free of charge for Windows, MacOS, and Linux. The user can upload and process the data entirely locally on their machine by specifying the desired mass-to-charge ratios of the targeted compound ions and simply clicking "Process". It allows for the processing of multiple files simultaneously, freely modifying and exporting graphs in real time, and calculating compound concentrations based on calibration standards. We show the versatility and applicability of LCMSpector to different kinds of mass spectrometry data by analyzing a series of publicly available datasets from various samples recorded on instruments from multiple vendors and by different research teams.
    DOI:  https://doi.org/10.1371/journal.pcbi.1013095
  27. J Chromatogr A. 2025 Dec 03. pii: S0021-9673(25)00948-3. [Epub ahead of print]1766 466604
    Quantitative profiling of aromatic amino acids and their host-microbial co-metabolites in human urine via UPLC-MS/MS.
    Domniki Gallou, Olga Begou, Helen Gika, Vasiliki Sarli, Ian D Wilson, Georgios Theodoridis.
      The aromatic amino acids tryptophan, tyrosine and phenylalanine are involved in many biochemical pathways and their metabolism and co-metabolism by the human and the gut microbiota results in the production of a number of metabolites. Many of these are phenols which are excreted in the urine after either sulfation or glucuronidation by the host. These metabolic processes can be dysregulated due to factors such as inflammation, disease, dietary and/or pharmaceutical interventions. Validated, quantitative methods for the analysis of aromatic amino acids and their metabolites may therefore provide insights into host-gut microbiota symbiosis and its association with pathological conditions. As sulfation is often the favored form of conjugation for phenolic compounds, the development of analytical methods would benefit from access to the sulfate conjugates as reference standards, which unfortunately are scarce. To overcome this limitation nine sulfate conjugates were synthesized using standard chemical routes and were subsequently purified by preparative HPLC. Following structure confirmation (1H NMR and MS/MS analysis) the standards were used along with 24 other analytes for the development and validation of a quantitative LC-MS/MS-based assay. The method used a CSH Phenyl-Hexyl column to separate and analyze 33 aromatic amino acids and their metabolites in urine. The method was validated and subsequently applied to the analysis of urine obtained from 20 healthy individuals to obtain information on the relevant concentrations in human urine.
    Keywords:  Aromatic amino acids; Chemical synthesis; Gut microbiota; LC-MS/MS; Method development; Sulfated metabolites
    DOI:  https://doi.org/10.1016/j.chroma.2025.466604
  28. Commun Chem. 2025 Dec 17.
    Structure characterization with NMR molecular networking.
    Cailum M K Stienstra, Jaegun Song, David Healey, Gennady Voronov, Eric Gardner, Abhishek Patel, Venkat Macherla, Christoph A Krettler, Tobias Kind, Pieter C Dorrestein, Daniel Domingo-Fernández.
      Nuclear Magnetic Resonance (NMR) is among the most widely used techniques for structure determination, yet automated workflows remain underdeveloped compared to mass spectrometry. In this work, we introduce NMR molecular networking and apply it to Heteronuclear Single Quantum Coherence (HSQC) spectra, a key 2D-NMR experiment for structure elucidation. We adapt core principles of MS² networking such as transitivity across multiple spectra, dereplication, and annotation propagation to NMR-driven workflows. First, we develop a modified Hungarian distance metric for HSQC peak matching. Benchmarks show that using this metric, traditional spectral lookup with this score recovers ~70-80% of available structural similarity, but efficiency does not improve when increasing the size of the spectral library. Second, we establish NMR molecular networking using HSQC spectra to propagate annotations and dereplicate compounds. Case studies of experimental natural product spectra demonstrate that annotation transitivity within networks accelerates and improves identification of unknowns. Third, we introduce algorithmic molecular networking, which integrates graph topology metrics to correct inefficient rankings and reduce false positives. Together, these approaches define the first generalizable framework for NMR molecular networking, enabling scalable, high-throughput annotation for natural product discovery and drug development.
    DOI:  https://doi.org/10.1038/s42004-025-01839-x
  29. J Chromatogr Sci. 2025 Nov 15. pii: bmaf063. [Epub ahead of print]63(10):
    Bioanalytical HPLC Method for Quantification of Benidipine in Rat Plasma: Stability and Application to Pharmacokinetic Study.
    Khater Al-Japairai, Samah Hamed Almurisi, Ayah Rebhi Hilles, Nadiya Abdul-Halim, Syed Mahmood.
      Benidipine is a dihydropyridine calcium channel blocker widely used in management of hypertension, and its pharmacokinetic evaluation requires reliable quantification in plasma. Even though liquid chromatography-mass spectrometry methods are available, simple and cost-effective HPLC approaches for determining benidipine in rat plasma remain limited. To address this gap, a reversed-phase high-performance liquid chromatographic (HPLC) method was developed and validated to assess the presence of benidipine in rat plasma. Acetonitrile was used as the extracting solvent for the liquid-liquid extraction of the plasma's analytes, followed by separation on an HPLC column. Benidipine's retention time was found to be 8.134 min. The limit of detection and the limit of quantification were determined to be, respectively, 0.016 μg/mL and 0.047 μg/mL. The method was validated over a liner (R2 = 0.9995) concentration range of 0.05 to 10 μg/mL. The level of precision and accuracy were found to be within acceptable limits. Benidipine was found to be stable under freeze-thaw and short-term conditions. Benidipine's pharmacokinetic parameters were suitably assessed in Sprague-Dawley rats after a single oral dosage (0.822 mg/kg). The findings demonstrated the suitability and applicability of the developed bioanalytical HPLC approach as a tool for the pharmacokinetic analysis of benidipine.
    DOI:  https://doi.org/10.1093/chromsci/bmaf063
  30. Anal Chem. 2025 Dec 17.
    Online Electroextraction-NanoESI-MS for Rapid Analysis of Catecholamines in Urine.
    Meng Zhang, Yanxiao Jiang, Qiong Wu, Hong Zhang, Kai Yu, Guangfeng Kan, Daqian Song, Jie Jiang.
      The direct mass spectrometric analysis of complex biological samples is often hindered by matrix interference and the need for extensive sample preparation. In this study, an online electroextraction method based on nano-electrospray mass spectrometry (OEE-nESI-MS) was proposed for the high-sensitivity and rapid analysis of urine samples. Compared with other methods, OEE-nESI-MS requires only 5 μL of sample and 35 μL of extraction solvent to achieve the migration and simultaneous ionization of the target from the sample solution to the extraction solvent in the nano tip, and online extraction and simultaneous analysis can be achieved within 8 min, while maintaining comparable sensitivity to other detection methods. The OEE-nESI-MS showed good linearity (R2 > 0.995) in the range of 1-600 ng mL-1 for the five catecholamines (CAs) in urine, with detection limits as low as 0.39-0.89 ng mL-1 with recoveries of 91.9-104.9% (RSD ≤ 8.9%). Exploration of the OEE-nESI mechanism emphasized the electric field applied as a key factor facilitating online electroextraction. The OEE-nESI-MS was successfully applied to the analysis of five CAs in real urine samples. This advancement provides a very simplified solution for the online rapid, highly sensitive, and quantitative determination of complex samples.
    DOI:  https://doi.org/10.1021/acs.analchem.5c05250
  31. J Agric Food Chem. 2025 Dec 16.
    Determination of Analytical Interferences for 4:2 Fluorotelomer Sulfonic Acid in Multiple Agricultural Matrices.
    Christine M Fisher, Brian Ng, Pierluigi Delmonte, Elsie Peprah, Samanta Popol, Wendy Young, Susan Genualdi.
      During analysis of corn snaplage, fiddleheads, and hay for per- and polyfluoroalkyl substances (PFAS) using a liquid chromatography-tandem mass spectrometry (LC-MS/MS) triple quadrupole method, a series of interferents were observed for 4:2 fluorotelomer sulfonic acid (4:2 FTS, m/z 326.9743). Liquid chromatography high-resolution mass spectrometry (LC-HRMS) and MS/MS were used to identify these interferents as corchorifatty acid F and other complex lipids capable of generating m/z 327.2177. Approaches to differentiate 4:2 FTS from these interferents included HRMS, scheduling alternate transitions in triple quadrupole methods to monitor for the presence of these interferents, and altering the chromatography conditions (e.g., C-18 vs C-18 PFP column). Importantly, reporting these findings and adding these interferents to the PFAS interference list (PIL) for 4:2 FTS raise awareness for the possibility of matrix interferences in these agricultural products and reduce future false positive and/or over-reporting of PFAS in complex samples.
    Keywords:  4:2 FTS; analytical interferents; corchorifatty acid F; corn snaplage; fiddleheads, hay; per- and polyfluoroalkyl substances (PFAS)
    DOI:  https://doi.org/10.1021/acs.jafc.5c12943
  32. PLoS One. 2025 ;20(12): e0326727
    Estrogen profiling in blood and brain: Effects of season and an aggressive interaction in a songbird.
    Cecilia Jalabert, Megan Q Liu, Kiran K Soma.
      Neuroestrogens are synthesized in the brain and regulate social behavior and cognition. In the song sparrow (Melospiza melodia), 17β-estradiol (17β-E2) promotes aggression, even during the non-breeding season, when circulating 17β-E2 levels are non-detectable. Measuring estrogens is challenging due to their low concentrations and the limited sensitivity of many existing assays. Moreover, estrogens other than 17β-E2 are often overlooked. Here, we developed a liquid chromatography tandem mass spectrometry (LC-MS/MS) assay for the simultaneous measurement of eleven estrogens using derivatization with 1,2-dimethylimidazole-5-sulfonyl-chloride (DMIS) to enhance sensitivity. We included four 13C-labeled internal standards, which corrected for matrix effects when measuring catecholestrogens and methoxyestrogens. This method is highly specific, sensitive, accurate, and precise, and improves upon our prior protocol, which could measure four estrogens with a single deuterated internal standard. Then, we applied the new method to samples from free-living adult male song sparrows to assess the effects of season and an aggressive encounter on blood and brain estrogens. Subjects were randomly assigned to either a 10-min simulated territorial intrusion (STI; song playback and live decoy) or a control condition (silent speaker and empty cage) during the breeding or non-breeding season, followed by rapid capture and immediate collection of blood and brain tissue. Only estrone and 17β-E2 were present in blood and brain, while the other nine estrogens in the panel were below detection limits. As expected, there was large regional variation in neuroestrogen levels and very low estrogen levels in blood. There was also large seasonal variation, and estrogen levels were lower in the non-breeding season. Despite robust aggression to the STI, estrogen levels did not differ between STI and control subjects in either season. In sum, our novel method enables ultrasensitive measurement of eleven estrogens and will be useful for studies of songbirds and other animals.
    DOI:  https://doi.org/10.1371/journal.pone.0326727
  33. Anal Chem. 2025 Dec 17.
    A Simple Online Internal Standard Calibration Strategy for Single-Particle Inductively Coupled Plasma Mass Spectrometry Based on Multielement Analysis.
    Xiangwei Tian, Ying Wang, Peijie Yang, Dingyi Wang, Yanwei Liu, Yingying Guo, Yuning Hu, Xiaoyan Zhang, Ligang Hu, Yongguang Yin, Yong Cai, Guibin Jiang.
      Single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS) is a powerful tool for resolving particle heterogeneity. However, in real environmental and biological samples, matrix effects pose significant challenges to accurate mass/size determination. Herein, we first systematically investigated the specific matrix effects on each stage of SP-ICP-MS analysis. Results showed that the sizes of Ag nanoparticles in the typical matrices were underestimated by nearly 10 nm due to 30-50% signal attenuation. To address this issue, we developed an online internal standard calibration strategy based on multielement detection and nonanalyte elements as internal standards. The theory of a novel calibration approach involving the use of nonanalyte elements as internal standards for signal response calibration was proposed and experimentally validated. The multielement detection mode was employed to measure the analyte (Ag) and internal standard elements (Pd and Au) within a single analytical run, enabling simultaneous correction of matrix-induced variations in signal response and nebulization efficiency. Under optimized time-resolution conditions (dwell time of 5 ms), the measured sizes of the particles in both simulated and real matrices showed good agreement with the true values. Overall, the proposed method provides a simple, reliable, and flexible solution for extending the applicability of SP-ICP-MS to the analysis of complex environmental and biological samples.
    DOI:  https://doi.org/10.1021/acs.analchem.5c06975
  34. Redox Biol. 2025 Nov 29. pii: S2213-2317(25)00466-5. [Epub ahead of print]89 103953
    Rapid quantitation of NAD+/NADH and NADPH/NADP+ with mass spectrometry by using calibration constants.
    Qiuyuan Guo, Mike Lingjue Wang, Michaela Schwaiger-Haber, Xiangfeng Niu, Shanshan Zhang, Leah P Shriver, Gary J Patti.
      NAD+/NADH and NADPH/NADP+ are important indicators of cellular redox status, but they cannot be reliably calculated from the relative intensities of mass spectrometry signals alone. Establishing accurate redox ratios by mass spectrometry has historically required converting relative signal intensities into absolute concentrations, which is a time-consuming process that limits rapid analysis. Here, we describe a simpler strategy to determine NAD+/NADH and NADPH/NADP+ by using mass spectrometry. While ionization is strongly influenced by factors such as instrument drift and sample type, we discovered that the relative signal intensities of oxidized and reduced cofactors change at the same rate across experiments performed on the same mass spectrometer. That rate can be experimentally determined and expressed as a calibration constant. Using calibration constants, relative intensities of mass spectrometry signals can be rapidly transformed into accurate redox ratios without the use of authentic standards or isotopically labeled internal standards. We present a metabolomics workflow to measure NAD+/NADH and NADPH/NADP+ by using calibration constants and compare the results to other methods, including commercial colorimetric assays. Although colorimetric assays are the most widely used, we demonstrate that mass spectrometry quantitation with calibration constants provides more accurate results.
    Keywords:  Calibration constants; LC/MS; Metabolomics; NAD(+)/NADH; NADPH/NADP(+); Nicotinamide adenine dinucleotide; Nicotinamide adenine dinucleotide phosphate
    DOI:  https://doi.org/10.1016/j.redox.2025.103953
  35. Sichuan Da Xue Xue Bao Yi Xue Ban. 2025 Sep 20. 56(5): 1197-1207
    [High-Throughput Detection of Multiple Classes of Antibiotics in Source Water Using a Functionalized Polyacrylonitrile Nanofiber Membrane].
    Kai Wang, Qixun Nian, Chunmin Wang, Qiuping Zhang, Qian Xu.
       Objective: To develop a novel solid-phase extraction (SPE) method based on a functionalized nanofiber membrane for the efficient co-extraction of structurally diverse antibiotics with markedly different physicochemical properties from source water, and to establish a high-throughput analysis method by coupling this technique with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS).
    Methods: A polydopamine and zirconium (Ⅳ) fumarate metal-organic frameworks (MOF-801) co-modified polyacrylonitrile nanofiber membrane (PDA@PAN/MOF-801 NFMs) was prepared as the SPE adsorbent through hybrid electrospinning and dopamine self-polymerization. Critical SPE and UPLC-MS/MS parameters were optimized, and the method was applied to analyze antibiotic contamination in source water samples from 14 sources of centralized drinking water supply in Suzhou, China, to evaluate the practical application potential of the method.
    Results: The PDA@PAN/MOF-801 NFMs adsorbent demonstrated efficient adsorption of 32 antibiotics from 6 classes through multiple retention mechanisms, including synergistic electrostatic interactions, hydrogen bonding, and π-π interactions. In combination with UPLC-MS/MS, the SPE method we developed enabled high-throughput detection of multiple antibiotics in source water, with limits of detection (LOD) being 0.001-0.05 ng/L and limits of quantitation (LOQ) being 0.005-500 ng/L. Spiked recoveries were 70.14%-111.50%. Intra-day relative standard deviation (RSD) was below 14.12% and the inter-day RSD was below 15.07%. The method demonstrated excellent sensitivity, accuracy, and precision.
    Conclusion: In this study, we successfully developed an efficient analytical method based on a novel nanofiber membrane adsorbent. This approach provides a new technical reference for the high-throughput detection of multiple antibiotics in environmental waters and shows promising potential for practical applications.
    Keywords:  Antibiotics; Nanofibers; Solid phase extraction; Tandem mass spectrometry; Water
    DOI:  https://doi.org/10.12182/20250960105
  36. J Pharm Sci. 2025 Dec 16. pii: S0022-3549(25)00589-1. [Epub ahead of print] 104135
    Ensuring pharmaceutical safety: Highthroughput LC-MS/MS method for plastic additive detection.
    İbrahim Hakkı Demircioğlu, Oğuzhan Dalkılıç, Saffet Çelik, Tugrul Cagri Akman, Hamdullah Kılıç, Levent Kandemir, Alptuğ Atila.
      Extractables and Leachables studies require highly reliable and sensitive analytical methods to ensure pharmaceutical product safety. Plastic additives are widely used during production to improve the physicochemical properties of polymeric products. However, these additives may constitute a potential toxicological risk by contaminating active pharmaceutical ingredients and pharmaceutical preparations. In this study, a short-term, sensitive, accurate, and reliable LC-MS/MS method was developed for the analysis of 15 plastic additives defined in the European Pharmacopoeia and validated in accordance with the ICH Q2(R2) guideline. An electrospray ionization source was used for the analyses in both negative and positive modes. Chromatographic separation was carried out using a reverse-phase phenyl C18 column and a mixture of methanol and ultrapure water containing 5 mM ammonium acetate as the mobile phase by the gradient elution method. As a result of method optimization, the flow rate and total analysis time were determined to be 0.7 mL/min and 15 minutes, respectively. Diphenyl phthalate was chosen as the internal standard. The LLOQ values of plastic additives were generally determined as 50 ng/mL (150 ng/mL for oleamide). The reliability of the method was verified by intraday/interday precision and accuracy analyses. Both extractable and leachable studies were performed using the developed method. It was effectively used to detect plastic additive contamination in pharmaceutical products such as bromobutyl stoppers, LDPE containers, disposable eye drop packaging, and polypropylene bags. The developed LC-MS/MS method was successfully applied to the analysis of pharmaceutical formulations containing 1.4% polyvinyl alcohol and 0.6% povidone, sodium hyaluronate, salbutamol sulfate, and 0.9% isotonic sodium chloride.
    Keywords:  Extractables & Leachables; LC-MS/MS; packaging materials; pharmaceuticals; plastic additives; validation
    DOI:  https://doi.org/10.1016/j.xphs.2025.104135
  37. Bioinformatics. 2025 Dec 17. pii: btaf660. [Epub ahead of print]
    OmicsQ: A User-Friendly Platform for Interactive Quantitative Omics Data Analysis.
    Xuan-Tung Trinh, André Abrantes da Costa, David Bouyssié, Adelina Rogowska-Wrzesinska, Veit Schwämmle.
       MOTIVATION: High-throughput omics technologies generate complex datasets with thousands of features that are quantified across multiple experimental conditions, but often suffer from incomplete measurements, missing values, and individually fluctuating variances. This requires analytical tools for accurate, deep and insightful biological interpretation, capable of dealing with a large variety of data properties and different amounts of completeness. Software capable of handling such data complexity and integrating with external applications for downstream analysis remains rare and mostly relies on programming-based environments, limiting accessibility for researchers without computational expertise.
    RESULTS: We present OmicsQ, an interactive, web-based platform designed to streamline quantitative omics data analysis. OmicsQ provides an intuitive, browser-based visualization interface that integrates established statistical processing tools. Those include robust batch correction, automated experimental design annotation, and handling of missing data without imputation, which maintains data integrity and avoids artifacts from a priori assumptions. OmicsQ seamlessly interacts with external applications (e.g., PolySTest, VSClust, ComplexBrowser) for statistical testing, clustering, analysis of protein complex behavior, and pathway enrichment, offering a comprehensive and flexible workflow from data import to biological interpretation that is broadly applicable across domains.
    AVAILABILITY AND IMPLEMENTATION: OmicsQ is implemented in R and Shiny and is available at https://computproteomics.bmb.sdu.dk/app_direct/OmicsQ. Source code and installation instructions: https://github.com/computproteomics/OmicsQ, DOI: 10.5281/zenodo.17778420.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaf660
  38. FEBS Lett. 2025 Dec 16.
    Analytical methods and tools for studying inositol phosphates.
    Masatoshi Ito, Shinichi Koguchi, Adolfo Saiardi, Eiichiro Nagata.
      Despite numerous studies, the biological and medical significance of inositol phosphates (InsPs) remains to be fully elucidated. One of the primary rate-limiting factors for InsP research is the difficulty in developing a method to specifically detect these molecules in complex biological matrices. Recent remarkable advancements in analytical chemistry such as nuclear magnetic resonance spectroscopy, mass spectrometry, and pertinent separation technologies have allowed the selective and sensitive differentiation of InsPs depending on the number and/or position of phosphate groups bound to the inositol ring. Thus, knowledge and experience of analytical chemistry have increasingly become a prerequisite for InsP studies. Establishing synthetic processes for functional InsPs and their analogs by organic chemists has also provided effective tools for quantitating their absolute abundances, as well as for investigating their molecular functions. This review briefly recapitulates the historical trajectory of the methodology applied to InsP research and highlights recently developed protocols using mass spectrometry coupled with liquid chromatography and capillary electrophoresis, in addition to a simple description of the chemical and chemoenzymatic synthesis of InsPs and their analogs.
    Keywords:  capillary electrophoresis–mass spectrometry; inositol phosphate; inositol pyrophosphate; isotope labeling; liquid chromatography–mass spectrometry; mass spectrometry; phosphoramidite chemistry
    DOI:  https://doi.org/10.1002/1873-3468.70246
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