bims-metlip 2026-04-12 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2026–04–12
24 papers selected by
Sofia Costa, Matterworks

Azetidination-based photocycloaddition enables regioisomer-resolved annotation of cholesteryl esters by negative-ion-mode LC-MS/MS.
A unified UPLC-MS/MS method for simultaneous quantification of intact anthocyanins and their metabolites in rat plasma.
Determination of Encapsulated and Unencapsulated Amphotericin B in Dog Plasma by LC-MS/MS Coupled With a Simple and Efficient Solid-Phase Extraction: Application to a Pharmacokinetic Study of Liposomal Amphotericin B.
A Novel Multimodal LC-MS/MS Panel for the Comprehensive Diagnosis of Neurometabolic Disorders in CSF.
Development and Validation of an LC-MS/MS Method for Quantitative Determination of Tacrolimus in Mouse Serum.
Rapid Analysis of NAD and Other Phosphorylated Metabolites in Complex Biological Samples by Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry.
Development of a Quantitative Serial LC-MS/MS Method for Gut Microbiota Metabolomics.
Development and validation of a 34-analyte urine quantitative LC-MS/MS toxicology panel.
A Chemically Derivatized in Silico Mass Spectral Library for Fine-Structure Annotation of Phosphoinositides.
Non-decalcified human teeth sample preparation method for MALDI mass spectrometry imaging.
Optimized cleanup strategy for the determination of bisphenols in human serum with Na86(AlO2)86(SiO2)106 as sorbents: Molecular insights and critical factor evaluation.
Metabolomics across scales: from single cells to population studies.
Untargeted metabolomic data of some Indonesian seaweed species (Halymenia durvillei, Gracilaria gigas, Caulerpa racemosa, and Palmaria palmata).
Simultaneous quantification of Amadori and Heyns compounds derived from the same amino acid in tobacco by HPLC-MS/MS with ion ratio strategy.
Development and validation of an online extraction HPLC-HRMS method for the quantification of carbapenems in FecalSwab™ samples.
Development and Evaluation of an LC-MS/MS Method for Determining Paraquat and Diquat in Human Plasma: a Retrospective Study.
Pan-Metabolomics Repository Mapping of the Carnitine Landscape.
A Novel Ultra-Performance Liquid Chromatography-Electrospray Ionisation-Tandem Mass Spectrometry Method for Quantification of Imeglimin in Human Plasma: Application to a Bioequivalence Study.
Investigation into oximation methods to improve the selective detection of small α-ketoacids in cell extracts by GC-EI-MS.
3-EPI-25-HYDROXYVITAMIN D3 INTERFERENCE IN ASSAYS FOR THE MEASUREMENT OF 25-HYDROXYVITAIMN D3.
High-Throughput Small-Scale Platform for Synthesis, Characterization, and Modeling of Per- and Polyfluoroalkyl Substances Analogs.
A practical framework for super-resolution of mass spectrometry images via adaptation of deep learning models.
Value Assignment of Vitamin D and 25-Hydroxyvitamin D in Food-Matrix Standard Reference Materials (SRMs) Using Isotope Dilution Liquid Chromatography-Tandem Mass Spectrometry (ID LC-MS/MS).
Standardized ready-to-use natural deep eutectic solvent-impregnated polypropylene fiber units for robust and high-throughput determination of tyrosine kinase inhibitors in biological fluids.

Anal Chim Acta. 2026 Jun 08. pii: S0003-2670(26)00342-9. [Epub ahead of print]1402 345392

Azetidination-based photocycloaddition enables regioisomer-resolved annotation of cholesteryl esters by negative-ion-mode LC-MS/MS.

Andrea Cerrato, Enrico Taglioni, Chiara Cavaliere, Aldo Laganà, Elena Lucà, Carmela Maria Montone, Anna Laura Capriotti.

   BACKGROUND: Cholesteryl esters (CE) play central roles in lipid transport and storage, yet their structural characterization remains challenging due to their extreme hydrophobicity and poor ionization efficiency. Conventional CE lipidomics workflows typically rely on positive-ion-mode analysis and report CE at the sum-composition level, without resolving double-bond (C]C) positional isomerism. Chemical derivatization strategies enabling isomer-resolved analysis of CE are therefore highly desirable but remain largely unexplored.
RESULTS: In the present study, the use of the aza-Paternò-Büchi (aPB) reaction with 6-azauracil was extended to CE, enabling negative-ion-mode LC-HRMS/MS analysis with annotation of C]C bond regiochemistry. Optimization of the derivatization conditions allowed efficient reaction of highly hydrophobic CE while maintaining compatibility with electrospray ionization. Tandem mass spectrometry revealed a previously unreported set of diagnostic fragment ions that proved particularly suitable for quantitative applications. The workflow enabled both relative and absolute quantitation of CE regioisomers with good linearity, repeatability, and trueness over a wide dynamic range, using a single dominant diagnostic ion to simplify data processing. Application to complex biological matrices of clinical interest demonstrated the feasibility of the approach, providing direct access to CE regioisomer distributions in human plasma and bovine liver.
SIGNIFICANCE: This study establishes aPB-based derivatization as a viable and complementary strategy for structurally resolved CE analysis, expanding the analytical toolbox for lipidomics studies where detailed molecular structure is critical for biological interpretation.

Keywords:  Aza-Paternò-Büchi; Double bond location; High-resolution mass spectrometry; Lipidomics

DOI:  https://doi.org/10.1016/j.aca.2026.345392
Anal Methods. 2026 Apr 07.

A unified UPLC-MS/MS method for simultaneous quantification of intact anthocyanins and their metabolites in rat plasma.

Chunzi Zhang, Guzhalinuer Aierken, Xiaoyan Ma, Tuxia Pang, Juan Zhang, Mihriban Arken, Shuyong Yu, Qianghui Mian, Xiaoli Ma.

A rapid and sensitive UPLC-MS/MS method was established and validated for the simultaneous quantification of mulberry anthocyanins and their major metabolites in rat plasma. The method successfully achieved, for the first time, the simultaneous quantification of anthocyanin prototype compounds, including cyanidin-3-O-glucoside (C3G) and cyanidin-3-O-rutinoside (C3R) and their major metabolites, namely protocatechuic acid (PCA), 4-hydroxybenzoic acid (4-HBA), p-coumaric acid (p-CA), and vanillic acid (VA) in the same analysis. Plasma samples were prepared using a straightforward protein precipitation procedure with methanol, followed by chromatographic separation on a Waters ACQUITY Premier BEH C18 column under gradient elution conditions. Quantitative analysis was performed in multiple reaction monitoring (MRM) mode using electrospray ionization in both positive and negative ion modes, with an internal standard for calibration. Method validation covered specificity, linearity, limits of detection and quantification, precision, recovery, and stability. All analytes exhibited satisfactory linearity with correlation coefficients (R2) exceeding 0.990. Limits of quantitation of the method were 0.25-10.00 ng mL-1. Within- and between-day precisions ranged from 2.40% to 15.73% and 4.95% to 16.92%, respectively, and extraction recoveries were in the range of 81.95-99.74%. Under various conditions tested, all compounds were stable for at least 6 h. The method was demonstrated to be simple, sensitive, selective, and robust, and was successfully applied for the determination of anthocyanins and their metabolites in rat plasma after oral administration. These results would be beneficial for the pharmacokinetic and metabolic research of anthocyanins in complex biological matrices.

DOI: https://doi.org/10.1039/d6ay00186f
Biomed Chromatogr. 2026 May;40(5): e70444

Determination of Encapsulated and Unencapsulated Amphotericin B in Dog Plasma by LC-MS/MS Coupled With a Simple and Efficient Solid-Phase Extraction: Application to a Pharmacokinetic Study of Liposomal Amphotericin B.

Haiyan Xu, Jing Zhuo, Huanyu Wei, Ruihan Ma, Xingyue Zhang, Aiping Yu, Yanan Zhang, Xiumei Lu.

  A convenient and reliable SPE method coupled with a specific and sensitive LC-MS/MS technique was developed and validated for the separation and determination of unencapsulated amphotericin B (F-AMB) and encapsulated amphotericin B (L-AMB) in dog plasma. L-AMB and F-AMB in the biomatrix were simultaneously separated by Oasis HLB SPE column using natamycin as the internal standard (IS). Chromatographic separation was achieved on a ZORBAX Eclipse XDB C18 column with gradient elution at a flow rate of 0.5 mL/min. The mobile phase consisted of methanol (0.1% formic acid) and a 5-mM ammonium acetate solution (0.1% formic acid). Mass spectrometry detection was performed in positive ion mode with an electrospray ionization source. Apart from regular quality control (QC) samples, a series of cross-QCs was adopted to verify the specificity and reproducibility of the quantification. We showed that F-AMB and L-AMB were completely separated without mutual interference in the quantitative linearity ranges of F-AMB and L-AMB, which were 10.0-800 and 100-25,000 ng/mL, respectively. The method was then applied to a pharmacokinetic study of liposomal amphotericin B in beagle dogs, and excellent ISR results were obtained for both L-AMB and F-AMB assays.

Keywords:  LC–MS/MS; SPE separation; amphotericin B; encapsulated and unencapsulated drug; liposomal drug

DOI:  https://doi.org/10.1002/bmc.70444
J Inherit Metab Dis. 2026 May;49(3): e70167

A Novel Multimodal LC-MS/MS Panel for the Comprehensive Diagnosis of Neurometabolic Disorders in CSF.

Stine Christ, Julia Rossmann, Sylvia Richter, Sven Garbade, Glynis Klinke, Nenad Blau, Georg Friedrich Hoffmann, Jürgen Günther Okun, Thomas Opladen.

  Metabolic testing of cerebrospinal fluid (CSF) is essential for early diagnosis of neurometabolic disorders. However, the large number of differential diagnoses, the phenotypic variance within a clinical picture, and the disease rarity complicate targeted metabolic diagnostics. To improve diagnosis the aim is to establish a liquid chromatography-tandem mass spectrometry (LC-MS/MS) based CSF panel (NeuroMetabolom) which enables a quick, reliable, extensive and cheap method requiring small amounts of analysis material replacing classical single platform analyses. The novel LC-MS/MS NeuroMetabolom method enables measuring all known standard metabolites in CSF, including purines/pyrimidines, sepiapterin, γ-Aminobutyric acid (GABA), and vitamin B6 metabolites, with significantly reduced sample volume and measurement time. Due to their different biochemical interactions several runs with different sample preparation, running time and columns are necessary within the LC-MS/MS. Age-dependent reference values have been established. Positive controls with consistently detectable metabolite patterns were used to assess analytical reliability. The method has been implemented into routine diagnostics practice. The LC-MS/MS panel enables a simple, comprehensive, and rapid diagnostic approach, reducing time to diagnosis and facilitating early initiation of treatment. Instead of 650 μL, only 250 μL CSF is now required and the analysis time for all metabolites is reduced from 280 to 65.3 min excluding preparation and setup time. Furthermore, the panel is adaptable and can be regularly expanded to include additional clinically relevant metabolites. The novel LC-MS/MS panel, together with a neurometabolomic approach, offers a promising avenue to timely clinical diagnosis. Trial Registration: German Clinical Trials Register: DRKS00007878.

Keywords:  CSF; LC–MS/MS; NeuroMetabolom; neurotransmitter; panel; targeted metabolomics

DOI:  https://doi.org/10.1002/jimd.70167
Biomed Chromatogr. 2026 May;40(5): e70437

Development and Validation of an LC-MS/MS Method for Quantitative Determination of Tacrolimus in Mouse Serum.

Xiaoming Wang, Madhuri Tatiparthy, Tilu Jain Thomas, Vinoshana Sama, Ramkumar Menon, Ananth Kumar Kammala.

  Tacrolimus, a potent immunosuppressant with a narrow therapeutic index, is a known substrate of P-glycoprotein (P-gp), a key efflux transporter involved in drug disposition. Accurate and sensitive quantification of tacrolimus in small-volume mouse serum is essential not only for pharmacokinetic studies but also for evaluating in vivo P-gp functional activity, particularly in pregnancy-related drug transport research. Tacrolimus was extracted using methyl tert-butyl ether after alkalization of the serum with NH₄OH. Chromatographic separation was achieved on a C18 HPLC column with a mobile phase of acetonitrile and water containing 0.2% NH₄OH. Detection was performed in negative ion mode using multiple reaction monitoring (MRM) transitions of m/z 802.5 → 560.6 for tacrolimus and m/z 805.5 → 563.6 for the internal standard, tacrolimus-13C,d2. The calibration range for tacrolimus was 0.26-44.8 ng/mL. The method demonstrated good precision, with intra- and inter-day relative standard deviations below 12%, and accuracy ranging from 94% to 103%. Compared to previously published methods, this approach requires only 200 μL of mouse serum and provides high sensitivity, with a lower limit of quantification of 0.26 ng/mL. The assay showed high sensitivity, minimal matrix interference, and good stability across tested conditions.

Keywords:  LC–MS/MS; alkalization; mouse serum; quantitative determination; tacrolimus

DOI:  https://doi.org/10.1002/bmc.70437
Anal Chem. 2026 Apr 08.

Rapid Analysis of NAD and Other Phosphorylated Metabolites in Complex Biological Samples by Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry.

Adela Pravdova, Maximilian Kleinert, John Henderson, Eleni Kafkia, David Pladevall-Morera, Caio Y Yonamine, Jonas T Treebak, Tetiana Brodiazhenko, Ilya Terenin, Jan Jakub Zylicz, Thomas Moritz, Ondrej Hodek.

Nucleotides and coenzymes play critical roles in energy metabolism and cellular signaling and as building blocks of nucleic acids. This work addresses the challenges in the measurement of the phosphorylated metabolites using hydrophilic interaction liquid chromatography coupled with mass spectrometry, which facilitates the separation and detection of polar metabolites. Here, we present optimized HILIC-MS/MS methods for rapid analysis of polar metabolites including nucleotides and their derivatives in complex biological matrices, such as murine adipose, skeletal, and liver tissues, human plasma, and bacteria. The developed methodologies enable separation of key nucleotides and other phosphorylated metabolites within 6 min and cofactors such as NAD+, NADH, NADP+, and NADPH within 4 min. Validation of these methods demonstrated high accuracy, precision, and sensitivity and stresses the substantial impact of matrix effects. The applicability of the methods was also tested on 13C-labeling experiments with mouse pluripotent stem cells. Additionally, sample pretreatment techniques, such as liquid-liquid extraction and solid-phase extraction, were evaluated as a tool to decrease the negative impact of matrix effects in complex samples. This work enhances the analytical capabilities for nucleotide quantification in metabolomics, facilitating the study of metabolic pathways and disease markers.

DOI: https://doi.org/10.1021/acs.analchem.6c00721
ACS Omega. 2026 Mar 31. 11(12): 19431-19439

Development of a Quantitative Serial LC-MS/MS Method for Gut Microbiota Metabolomics.

Takanobu Yoshida, Tomoya Shintani, Daisuke Sasaki, Christopher J Vavricka, Yasushi Matsuki, Akihiko Kondo, Tomohisa Hasunuma.

The significance of gut microbiota in human health has gained increasing attention. Accordingly, metabolomics has been used to elucidate host-microbiota interactions. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an ideal choice for metabolome analysis of gut microbiota due to its quantitative capabilities. However, conventional LC-MS/MS requires multiple columns, multiple mobile phases, and complex procedures to optimize conditions for each target metabolite. To address these limitations, we developed a quantitative serial LC-MS/MS method, termed the Kobe University Serial LC-MS/MS Analysis using Multiple columns with a Single mobile phase (KUSLAMS). This platform integrates two columns (PFPP and C18) and a derivatization method for seamless, high-throughput quantification of 215 metabolites, including amino acids, nucleotides, carboxylic acids, amines, and fatty acids. Reproducibility for repeated analysis was assessed using 82 intracellular gut microbiota metabolites, for which new analytical methods were developed. Among these, 64 metabolites were detected with coefficients of variation (CV) below 15%. The application of KUSLAMS to an in vitro gut microbiota culture system with and without inulin revealed differences in the concentrations of 21 intracellular and 14 extracellular metabolites. Notably, several metabolites exhibited increased intracellular and decreased extracellular concentrations, suggesting a possible link between intracellular accumulation and extracellular depletion, although this interpretation is exploratory. These results indicate that KUSLAMS allows for the simultaneous monitoring of intra- and extracellular metabolite dynamics. Together, these findings demonstrate that KUSLAMS is a robust and versatile platform for the exploration of microbiota-derived metabolites relevant to human health.

DOI: https://doi.org/10.1021/acsomega.5c12997
J Chromatogr B Analyt Technol Biomed Life Sci. 2026 Apr 01. pii: S1570-0232(26)00137-6. [Epub ahead of print]1277 125048

Development and validation of a 34-analyte urine quantitative LC-MS/MS toxicology panel.

Adam Kutnick, Richard Giles, Adam J McShane.

  Expeditious and accurate drug testing of urine specimens supports clinical operations ranging from pain management to emergency medicine. Tandem mass spectrometry when used in conjunction with chromatography (LC-MS/MS) is a highly specific and sensitive technique that can simultaneously quantify numerous analytes of interest, providing notable advantages in sensitivity and specificity over other technologies such as immunoassays. We describe the development and validation of a clinical LC-MS/MS toxicology panel for quantitation of 34 drugs and metabolites that combines two predecessor methods, simplifying our workflow and adding several analytes not previously detected in either method. Validation work encompassed an alternative matrix mixing study and characterization of potential matrix effects as well as determination of analytical measurement range, analytical sensitivity, analytical specificity, carryover, precision, stability, accuracy, and hydrolysis efficiency. Limits of quantitation achieved ranged from 1 to 25 ng/mL at the lower end and 2000 to 5000 ng/mL at the upper end.

Keywords:  Clinical; Confirmation; Drugs of abuse; LC-MS/MS; Toxicology; Urine; Validation

DOI:  https://doi.org/10.1016/j.jchromb.2026.125048
Anal Chem. 2026 Apr 05.

A Chemically Derivatized in Silico Mass Spectral Library for Fine-Structure Annotation of Phosphoinositides.

Zhengjiu An, Ye Liu, Jian Ni, Jun Ding.

Phosphoinositides (PIPx) are structurally complex lipids with essential roles in cellular signaling and disease. Their biological functions critically depend on subtle molecular characteristics, including headgroup identity, acyl-chain composition, and regioisomerism. However, comprehensive structural annotation of PIPx species by mass spectrometry remains challenging due to their intrinsically low abundance, extensive isomerism, and limited availability of reference spectra. Herein, we report a chemically derivatized in silico mass spectral library that enables the fine-structure annotation of PIPx. A chemical derivatization strategy using (4-(diazomethyl)phenyl)-N,N-dimethylmethanamine (DMPDA) markedly improves the liquid chromatographic behavior and ionization efficiency of PIPx species, resulting in up to a 10-fold increase in detection sensitivity. More importantly, the resulting DMPDA-PIPx derivatives exhibit reprogrammed fragmentation behavior in tandem mass spectrometry, generating diagnostic ions that differentiate phosphate positional isomers as well as acyl-chain composition and sn-positional variants. General fragmentation rules were established and applied to 1,736,028 simulated DMPDA-PIPx structures, yielding an in-depth in silico mass spectral library that spans millions of PIPx structures. Integration of chemical derivatization with in silico library-based spectral matching enables automated annotation of PIPx isomers that are indistinguishable using conventional MS/MS approaches. Application of this workflow to aging mouse tissues reveals pronounced organ-specific heterogeneity in PIPx profiles and distinct tissue-specific remodeling of PIPx isomers during aging.

DOI: https://doi.org/10.1021/acs.analchem.6c00638
Anal Chim Acta. 2026 Jun 08. pii: S0003-2670(26)00336-3. [Epub ahead of print]1402 345386

Non-decalcified human teeth sample preparation method for MALDI mass spectrometry imaging.

Kayle J Bender, Joanna E Spurgeon, Chuo Ying Zhai, Manish Arora, Elizabeth K Neumann.

BACKGROUND: Human teeth preserve a rich temporal record of biological and environmental information throughout an individual's life. Accessing this record requires analytical techniques capable of providing both spatial and chemical resolution. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) offers powerful capabilities for visualizing the spatial distribution of biomolecules. However, successful analysis demands preservation of both morphology and chemical integrity. The hard and brittle nature of enamel and dentin presents a major challenge, as preparing sufficiently thin sections typically requires decalcification, which can compromise molecular content.
RESULTS: In this study, we present a sample preparation method using cryofilm, embedding, and specific cryostat blade angles to enable the analysis of non-decalcified human teeth by MALDI MSI. We further demonstrate this approach using various MALDI matrices, highlighting the potential of this technique for spatial analysis of biomolecules in teeth.
SIGNIFICANCE: This method provides a foundation for future investigations into the spatial and temporal distribution of small molecules in human teeth.

DOI: https://doi.org/10.1016/j.aca.2026.345386
Anal Chim Acta. 2026 Jun 08. pii: S0003-2670(26)00346-6. [Epub ahead of print]1402 345396

Optimized cleanup strategy for the determination of bisphenols in human serum with Na86(AlO2)86(SiO2)106 as sorbents: Molecular insights and critical factor evaluation.

Jing Jin, Cuicui Guo, He Zhang, Tian Tian, Bairong Fu, Longxing Wang, Dongqin Tan, Jiajia Yang, Ningbo Geng, Jiping Chen.

   BACKGROUND: Bisphenols, as ubiquitous environmental contaminants, pose significant public health concerns owing to their endocrine-disrupting properties. While liquid chromatography-tandem mass spectrometry is the gold standard for their trace-level quantification in biological matrices, its accuracy is fundamentally limited by substantial matrix effects. The development of separation techniques and analytical method for human biomonitoring will significantly advance human health risk assessment. The complexity of biological matrices and low concentrations of targets are the main challenges for human biomonitoring. Developing accessible and economic SPE sorbents suitable for the cleanup of serum is pivotal for conducting large-scale epidemiological and toxicological studies of BPs.
RESULTS: We present a cleanup protocol based on a 13X-type Na86(AlO2)86(SiO2)106 zeolite, and it achieved consistent and acceptable matrix effect suppression (63.3%-121%), outperforming commercial alternatives like C18 (15.0%-107%), HLB (4.5%-87.7%), and PEP-2 (8.9%-142%). Correlation analysis suggested that analyte recovery was significantly associated with logKow (P < 0.01) and positively correlated with estimated molecular volume. Combining the binding energy analysis, our finding suggested the role of shape selectivity and strong interaction (e.g. hydrogen bond interaction, electrostatic interaction) within the zeolite pores. The developed method was validated with bovine serum, demonstrating acceptable sensitivity (0.075-0.39 ng mL-1), precision (2.2%-18.0%), and accuracy (71.4%-124%). Its reliability for human biomonitoring was further evaluated by the good agreement with a reference method via Bland-Altman analysis.
SIGNIFICANCE: The zeolite-based SPE protocol demonstrates good selectivity and robustness, establishing it as a superior sample preparation technique for the biomonitoring of BPs in serum. It is feasible for the accurate assessment of the human internal exposure to BPs. In addition, our work identifies critical factors influencing extraction efficiency and molecular interactions via multiple regression analysis and molecular simulation, thereby providing a possible mechanistic insight.

Keywords:  Bisphenol; Cleanup; Mechanism; Molecular sieve; Solid-phase extraction

DOI:  https://doi.org/10.1016/j.aca.2026.345396
Nature. 2026 04;652(8109): 313-320

Metabolomics across scales: from single cells to population studies.

Theodore Alexandrov, Nicola Zamboni.

Metabolomics has matured into a powerful approach for probing metabolism, offering readouts that closely reflect cellular and organismal function in health and disease. Here we highlight two rapidly advancing frontiers: single-cell metabolomics and population-scale metabolomics. Single-cell metabolomics resolves the metabolic states of individual cells, uncovering cell-to-cell heterogeneity and spatial organization within tissues. Population-scale profiling profiles metabolites across large cohorts, enabling the discovery of markers of disease, environmental exposures and genetic variation. Although these approaches operate at different scales, they face shared challenges-including metabolite identification, quantification and multimodal data integration-and offer common advantages, such as the ability to capture non-genetic influences on phenotype and to scale to high throughput. We propose that continued advances in scalability will bring these domains together, enabling the construction of comprehensive metabolic atlases that chart cellular and interindividual variation and provide training data for foundation models of metabolism. By integrating cellular and population-level insights, single-cell and population-scale metabolomics promise to advance our understanding of metabolism across biology, medicine and pharmacology.

DOI: https://doi.org/10.1038/s41586-026-10277-1
Data Brief. 2026 Jun;66 112716

Untargeted metabolomic data of some Indonesian seaweed species (Halymenia durvillei, Gracilaria gigas, Caulerpa racemosa, and Palmaria palmata).

Dimar Sari Wahyuni, Komang G Wiryawan, Roni Ridwan, Mohamad Rafi, Gunawan Gunawan, Nurjanah Nurjanah, Susi Kusumaningrum, Sindu Akhadiarto, Galih Kusuma Aji, Dedi Noviendri, Tri Puji Priyatno, Eka Sari, Anuraga Jayanegara.

  This data article presents untargeted metabolomic data obtained from four Indonesian seaweed species: Halymenia durvillei, Gracilaria gigas, Caulerpa racemosa, and Palmaria palmata. Samples were collected from various coastal regions in Indonesia and processed using a standardized extraction protocol. Each seaweed sample was freeze-dried, ground, and extracted with methanol at a 1:20 (w/v) ratio, followed by sonication, filtration, and concentration through rotary evaporation. The extracts were analyzed with Liquid Chromatography-High Resolution Mass Spectrometry (LC- HRMS) using a Thermo Scientific UHPLC Vanquish Tandem Q Exactive Plus Orbitrap HRMS system. A C18 column and gradient elution profile, along with electrospray ionization in negative mode, were employed during analysis. Mass spectral data were processed with Compound Discoverer 3.3.2 software, and metabolite annotation were performed via MzCloud and ChemSpider databases. The dataset includes LC-HRMS spectral profiles and annotated metabolite features from six replicates per seaweed species. Principal component analysis (PCA) and heatmap analysis were performed on to group seaweed species with similar characteristics. A total of 31 putative metabolites were annotated and are available for further investigation. The PCA revealed that the segregation of the seaweeds was explained by a total variation of 92.6%, with PC1 and PC2 contributing 63.4% and 29.2%, respectively. A heatmap also provides prominent distinctive metabolite profiles among the four seaweeds. Associated metadata includes sampling locations with GPS coordinates, taxonomic classification, sample preparation protocols, LC-HRMS acquisition parameters, and data processing details. The dataset is publicly accessible through Figshare (DOI: 10.6084/m9.figshare.28658303.v1). This dataset can be reused for comparative metabolomics, biomarker discovery, nutritional profiling, or marine biodiversity research. It also supports researchers in pharmacology, marine biology, and bioinformatics who aim to explore or verify metabolite profiles of marine macroalgae using standardized high-resolution analytical techniques.

Keywords:  Liquid chromatography; Mass spectrometry; Primary metabolite; Seaweed extract

DOI:  https://doi.org/10.1016/j.dib.2026.112716
Talanta. 2026 Mar 30. pii: S0039-9140(26)00402-9. [Epub ahead of print]306 129746

Simultaneous quantification of Amadori and Heyns compounds derived from the same amino acid in tobacco by HPLC-MS/MS with ion ratio strategy.

Haoran Li, Shijun Xiong, Beibei Chen, Zhekuan Wu, Zhen Zhou, Yong Liang, Man He, Bin Hu.

  Amadori and Heyns compounds are key Maillard reaction intermediates, resulting from the reaction of a certain amino acid with glucose (Glu) or fructose (Fru), respectively. They play a dual role in augmenting cigarette aroma and attenuating sensory irritation, and their quantification in tobacco is vital for tobacco quality evaluation and Maillard reaction mechanism study. Currently, simultaneous quantification of Amadori and Heyns compounds derived from the same amino acid, which present as isomers, is encumbered by poor chromatographic separation, and reliance on unavailable specific fragment ions. Herein, a method based on high performance liquid chromatography combined with tandem mass spectrometry (HPLC-MS/MS) detection was developed for the simultaneous quantification of Amadori and Heyns compounds derived from the same three amino acids (alanine, proline, phenylalanine, abbreviated as Ala, Pro, and Phe, respectively) with an ion ratio strategy. Under the optimized conditions, the limits of detection ranging from 2.22 to 6.94 ng/mL were obtained for six target analytes (Fru-Phe/Glu-Phe, Fru-Pro/Glu-Pro, Fru-Ala/Glu-Ala). When the method was applied to tobacco leaf powder extracts, target Amadori and Heyns compounds were found in the range of 0.65-56.4 μg/g, with Heyns compounds consistently less abundant than Amadori counterparts. In the recovery test, target analytes showed recoveries of 76.8-111%. Compared with reported methods, the proposed method features universal applicability without requiring characteristic fragment ions or chromatographic separation. It provides a reliable tool for analyzing hard-to-separate sugar-derived Maillard intermediates in tobacco.

Keywords:  Amadori compounds; Heyns compounds; High performance liquid chromatography mass spectrometry; Ion ratio strategy; Maillard reaction

DOI:  https://doi.org/10.1016/j.talanta.2026.129746
J Pharm Biomed Anal. 2026 Mar 30. pii: S0731-7085(26)00157-3. [Epub ahead of print]277 117489

Development and validation of an online extraction HPLC-HRMS method for the quantification of carbapenems in FecalSwab™ samples.

Matthieu Holub, Assaf Mizrahi, Thibaut Genty, Benoit Pilmis, Alban Le Monnier, Nathalie Leveque.

  Quantifying carbapenems in fecal samples is analytically challenging due to their instability and the complexity of intestinal matrices. We developed and validated a novel HPLC-HRMS method enabling direct quantification of imipenem and meropenem in human fecal material collected with the FecalSwab™ system. Sample processing consisted of minimal handling, involving clarification and direct online extraction using TurboFlow™ prior to chromatographic separation on a reversed-phase column. Detection was performed using Orbitrap high-resolution mass spectrometry in full-scan mode. Because only a small fraction of parenterally administered carbapenems reaches the intestinal lumen, but even low concentrations can exert a strong ecological pressure on gut microbiota and promote selection of resistant Enterobacterales, sensitive measurement of residual fecal levels is essential to understand antibiotic-driven dysbiosis and resistance emergence. The method was validated according to ICH M10 guidelines. Linearity was achieved over 1.5-750 ng/L for imipenem and 2.9-1500 ng/L for meropenem (R² > 0.995). Trueness and precision were within ±15% at all QC levels (±20% at LLOQ). Matrix effects were controlled using isotopically labeled internal standards, yielding normalized matrix factors with CV < 12%. Stability studies confirmed rapid degradation of imipenem and moderate stability of meropenem in fecal medium, prompting the identification and semi-quantification of their hydrolysis products. The method was successfully applied to 40 clinical samples, detecting carbapenems or their degradation products in 17/20 imipenem-exposed and 18/20 meropenem-exposed patients. This validated workflow provides a robust and clinically applicable approach for assessing intestinal exposure to carbapenems and supports ecological investigations of antibiotic-microbiota interactions.

Keywords:  FecalSwab™; HPLC-HRMS method validation; antibiotic; antibiotic residues; carbapenem; microbiota

DOI:  https://doi.org/10.1016/j.jpba.2026.117489
Clin Lab. 2026 Jun 01. 72(3):

Development and Evaluation of an LC-MS/MS Method for Determining Paraquat and Diquat in Human Plasma: a Retrospective Study.

Jiayuan Wang, Bin Li, Ying Zhao, Limin Feng, Junshun Gao.

BACKGROUND: This study aimed to establish a high-performance liquid chromatography tandem mass spectrometry method for determining paraquat and diquat in human plasma and predict clinical outcomes.
METHODS: Each plasma sample was subjected to methanol protein precipitation and passed through a hydrophilic column and was then analyzed by mass spectrometry to determine paraquat and diquat. Receiver operating characteristic curves were used to calculate herbicide poisoning severity indices and allow herbicide concentrations in plasma to be used to predict clinical outcomes.
RESULTS: The responses to paraquat and diquat in plasma were strongly linear over the range of 20 - 10,000 ng/mL. The limit of quantitation and quality control samples met the required criteria. The paraquat and diquat poisoning severity index was significantly higher for the death group than the survival group (p < 0.05). The areas under the paraquat and diquat poisoning severity index receiver operating characteristic curves were 0.946 and 0.998, respectively, and the optimal clinical critical values were 22.84 and 15.64 (h·mg)/L, respectively, indicating good diagnostic performances for both herbicides.
CONCLUSIONS: The method is sensitive, accurate, quick, and specific, so it is highly recommended for clinical use.

DOI: https://doi.org/10.7754/Clin.Lab.2025.250311
bioRxiv. 2026 Mar 31. pii: 2026.03.27.714844. [Epub ahead of print]

Pan-Metabolomics Repository Mapping of the Carnitine Landscape.

Helena Mannochio-Russo, Patrick C Ferreira, Kine Eide Kvitne, Abubaker Patan, Victoria Deleray, Julius Agongo, Harsha Gouda, Wilhan D Gonçalves Nunes, Shipei Xing, Jasmine Zemlin, Martijn van Faassen, Erin R Reilly, Imhoi Koo, Andrew D Patterson, Shirley M Tsunoda, Mingxun Wang, Dionicio Siegel, Lindsey A Burnett, Pieter C Dorrestein.

Carnitines are a structurally diverse class of metabolites formed by conjugation of L-carnitine with fatty acids, amino acids, xenobiotics, and microbial metabolites. They play roles in transport, mitochondrial and peroxisomal metabolism, detoxification, and systemic signaling, yet their chemical diversity remains incompletely defined. We applied a pan-repository data mining strategy of LC-MS/MS data across GNPS/MassIVE, MetaboLights, and Metabolomics Workbench using MassQL diagnostic fragment ion filtering to systematically extract acylcarnitine spectra. This yielded a library of 34,222 unique MS/MS spectra representing 2,857 atomic compositions, corresponding to 3,872,050 detections. These datasets provide an MS/MS library for annotation, discovery, and contextualization of acylcarnitines, enabling identification of previously unknown carnitines, such as dihydroferulic acid conjugated carnitines and supporting future exploration of this metabolite class across host metabolism, diet, microbial activity, pharmacological exposures, and metabolic dysregulation.

DOI: https://doi.org/10.64898/2026.03.27.714844
Anal Sci Adv. 2026 Jun;7(1): e70079

A Novel Ultra-Performance Liquid Chromatography-Electrospray Ionisation-Tandem Mass Spectrometry Method for Quantification of Imeglimin in Human Plasma: Application to a Bioequivalence Study.

Mina Wadie, Kamal A Badr, Ahmed A Hosny, Liliya Logoyda, Omnia M El Sebai, Mamdouh R Rezk.

  The pharmaceutical market has recently witnessed the advent of a novel tetrahydrotriazene molecule belonging to the new pharmacological class "Glimins", named Imeglimin (IMG). It has been approved in Japan as a safe and highly effective oral diabetic drug for type II diabetic patients. It enhances the function of β-cells in the human pancreas and increases insulin sensitivity. Hence, this work was directed to provide a fast, sensitive and highly reliable bioanalytical method for its quantification in human plasma. What makes this work greatly distinctive is first: adopting an ultra-performance liquid chromatography (UPLC) with protein precipitation as a fast and straightforward sample preparation protocol with the highest extraction recovery. Secondly, utilisation of the stable isotope-labelled molecule, IMG-d6, rather than a structurally similar analogue, to avoid the interference of any co-administered drugs in human plasma. Samples were extracted with acetonitrile and then chromatographically separated using an Acquity UPLC BEH HILIC column of 1.7 µm particle size along with a mobile phase solution composed of 70:30 (v/v) acetonitrile and 10 mM ammonium formate buffer acidified with 0.1% formic acid. Upon adjusting the flow rate to 0.3 mL/min, IMG was eluted at 1.3 min with a total run time of only 2.0 min. Mass quantification was performed in positive electrospray ionisation operated in multiple reaction monitoring mode. IMG was quantified at m/z of 156.05 → 112.91 transition pairs while IMG-d6, at m/z 162.11 → 119.04. The proposed UPLC-tandem mass spectrometry method was thoroughly validated as per Food and Drug Administration principles over a linearity range of 10.0-3000.0 ng/mL and successfully applied for IMG quantification in human plasma samples. The scope of the work was extended to encompass real analysis of collected human blood samples, calculation of IMG pharmacokinetics parameters and conductance of a bioequivalence study between the IMG generic product versus brand one.

Keywords:  Imeglimin; UPLC‐MS/MS; bioequivalence study; pharmacokinetic study; protein precipitation

DOI:  https://doi.org/10.1002/ansa.70079
J Chromatogr B Analyt Technol Biomed Life Sci. 2026 Apr 05. pii: S1570-0232(26)00148-0. [Epub ahead of print]1277 125059

Investigation into oximation methods to improve the selective detection of small α-ketoacids in cell extracts by GC-EI-MS.

Sadie J Gale, Danisha Johal, Seth J Parker.

  Small α-ketoacids are important metabolic intermediates that influence metabolic states associated with disease. Measuring α-ketoacid levels and labeling in stable-isotope tracing studies using chromatography coupled to mass spectrometry is sometimes challenging due to their small mass, low cellular abundance, chemical instability, and enzymatic utilization post-quenching. Chemical derivatization is often employed to increase mass-to-charge, improve chromatographic separation in complex samples, and to stabilize α-ketoacids for detection by GC- or LC-MS. Methoximation is one of the most used derivatization strategies to modify α-keto groups present on metabolic α-ketoacids for GC-EI-MS. However, methoxime groups do not significantly increase analyte mass nor contribute to retention on the mid-polar GC columns widely used for metabolic labeling studies. In this study, we evaluate different oximation reagents to improve the selective detection of small α-ketoacid oxime-TBDMS derivatives by GC-EI-MS. We find that oximation using hydroxylamine, ethoxyamine, or O-benzylhydroxylamine offer comparable performance to methoxyamine with distinct effects on column retention and main fragment ion mass-to-charge. We also demonstrate how these approaches may be applied to cell extracts. Our results highlight hydroxylamine or O-benzylhydroxylamine as preferred derivatization reagents to increase alpha-ketoacid mass-to-charge or increase column retention, respectively.

Keywords:  Alpha-ketoacids; Gas chromatography; Mass spectrometry; Metabolomics; Stable-isotope tracing

DOI:  https://doi.org/10.1016/j.jchromb.2026.125059
J Steroid Biochem Mol Biol. 2026 Apr 08. pii: S0960-0760(26)00090-7. [Epub ahead of print] 107024

3-EPI-25-HYDROXYVITAMIN D3 INTERFERENCE IN ASSAYS FOR THE MEASUREMENT OF 25-HYDROXYVITAIMN D3.

Alex N Shaw, Emma L Williams.

  In chromatographic measurements of vitamin D, such as liquid chromatography tandem mass spectrometry (LC-MS/MS), 3-epi-25hydroxyvitamin D3 (3-epi-25OHD3) can interfere with 25-hydroxyvitamin D3 (25OHD3) quantification due to their identical mass. Chromatographic separation is therefore required to overcome this issue. In October 2024, the Vitamin D External Quality Assessment Scheme (DEQAS) distributed two serum samples: 664 (without exogenous 3-epi-25OHD3) and 665 (with 50 nmol/L of added 3-epi-25OHD3). Sample 664 yielded consistent results across 445 labs, giving an Trimmed Mean (ALTM) = 45.6 ± 6.1 nmol/L (±SD, CV=13.5%), aligning with the Centers for Disease Control and Prevention (CDC) reference value of 46.7 nmol/L. In contrast, sample 665 showed a higher ALTM of 62.1 ± 27.2 nmol/L (±SD, CV=43.9%) when compared to the CDC target value, with significant variability observed. Most automated immunoassays did not detect 3-epi-25OHD3, except for Roche Gen III (91% cross-reactivity) and Beckman DxI (39.8%). Among 90 LC-MS/MS laboratories reporting #665, 18 routinely measured 3-epi-25OHD3; 15 of these excluded it from their reported total 25OHD (method mean = 47 nmol/L) and 3 included 3-epi-25-OHD3, despite measuring both metabolites separately. The LC-MS/MS results showed a bimodal distribution, with 40 LC-MS/MS laboratories (44%) resolving the epimer chromatographically and 50 LC-MS/MS laboratories (56%) not effectively separating the epimer, leading to overestimation. This positive interference may have clinical implications, especially in neonates who naturally have high 3-epi-25OHD3 levels. Although its biological role remains unclear, current consensus advises excluding 3-epi-25OHD3 from total 25OHD when assessing vitamin D status.

Keywords:  3-epimer-25-hydroxyvitamin D; DEQAS; LC-MS/MS; cross-reactivity; interference; neonate; vitamin D

DOI:  https://doi.org/10.1016/j.jsbmb.2026.107024
Environ Sci Technol Lett. 2025 Oct 14. 12(10): 1437-1444

High-Throughput Small-Scale Platform for Synthesis, Characterization, and Modeling of Per- and Polyfluoroalkyl Substances Analogs.

Kai-Hung Huang, Namita Narendra, Kaili Yap, Nicolás M Morato, Kitmin Chen, Yunfei Feng, R Graham Cooks, Tillmann Kubis, Christina R Ferreira.

Per- and polyfluoroalkyl substances (PFAS) are a global challenge due to their exceptional thermal and chemical durability which leads to environmental persistence, bioaccumulation, and toxicity. Tackling this challenge is a complex endeavor as the ever-expanding number of emerging PFAS hinders their monitoring while current countermeasures remain limited. Thus, there is a need for rapid strategies that can transform PFAS into safer, degradable analogs or expand libraries for untargeted monitoring. Here, we describe the implementation of a high-throughput (1 Hz) desorption electrospray ionization mass spectrometry (HT-DESI-MS) platform for the chemical transformation of perfluorocarboxylic acids (PFCAs) via a data-driven workflow that led to 915 new PFCA analogs (89% success rate) and revealed reactivity trends. Tandem mass spectrometry (MS/MS) enabled online structural confirmation and diagnostic fragment identification, supporting standard-free LC-MS/MS analysis. Further integration with ion mobility spectrometry (IMS) provided drift time measurements correlating with molecular size and shape, adding a new dimension that can improve feature annotation in untargeted PFAS analysis. Complementary quantum mechanical calculations of dipole moment and HOMO- LUMO gap predicted polarity and electronic reactivity, guiding analog selection. Collectively, this workflow combines rapid synthesis, structural annotation, and multidimensional profiling, with potential to discover safer PFAS and enhance environmental monitoring.

DOI: https://doi.org/10.1021/acs.estlett.5c00699
Analyst. 2026 Apr 08.

A practical framework for super-resolution of mass spectrometry images via adaptation of deep learning models.

Yinghao Cao, Yuting Tan, Chang Li, Erping Long, Lin Wang.

Achieving high spatial resolution is critical for revealing tissue-specific metabolite distributions in mass spectrometry imaging (MSI), yet practical constraints often limit achievable resolution. While deep learning offers promising post-acquisition enhancement, the relative efficacy of different generative architectures for MSI data remains inadequately explored. This study establishes a comparative evaluation of three advanced deep learning architectures (SwinIR, MambaIR, and ResShift) against the established GAN-based model MOSR. Evaluated across three MSI datasets and six image quality metrics, MOSR and a bicubic pre-trained ResShift model demonstrated superior capacity in reconstructing complex textural details. Capitalizing on this, we developed a focused transfer-learning strategy to adapt the pretrained ResShift model using only ten mouse brain sagittal section images. The fine-tuned model achieved a 41.5% improvement in a composite performance score over its pre-trained state and a 14.0% improvement over MOSR. Remarkably, this model generalized effectively to distinct anatomical planes (horizontal brain sections) and entirely different tissue types (mouse kidney), as validated using multiple metabolites. Our work provides a benchmark for generative models in MSI super-resolution and proposes a practical, data-efficient fine-tuning framework that enhances image fidelity across diverse biological samples, offering a computational tool for spatially resolved metabolomics.

DOI: https://doi.org/10.1039/d6an00012f
J Agric Food Chem. 2026 Apr 04.

Value Assignment of Vitamin D and 25-Hydroxyvitamin D in Food-Matrix Standard Reference Materials (SRMs) Using Isotope Dilution Liquid Chromatography-Tandem Mass Spectrometry (ID LC-MS/MS).

Carolyn Q Burdette, James H Yen, Adam J Kuszak, Stephen A Wise.

  Discrepancies exist between reported vitamin D dietary intake and measured status. Hydroxylated metabolites such as 25-hydroxyvitamin D [25(OH)D] may be more bioavailable; however, information on 25(OH)D content in foods is limited. To address this gap and support analytical method validation, NIST value assigned vitamin D2, vitamin D3, and 25-hydroxyvitamin D3 [25(OH)D3] in five food-matrix Standard Reference Materials® (SRMs). Using isotope dilution LC-MS/MS, values were established for SRMs 1546a (Meat Homogenate), 1549a (Whole Milk Powder), 1577c (Bovine Liver), 1845a (Whole Egg Powder), and 3235 (Soy Milk). Mass fractions ranged from 0.498 μg/kg to 49.5 μg/kg for vitamin D3 and 0.53 μg/kg to 12.1 μg/kg for 25(OH)D3. These SRMs enable validation of analytical methods and measurement comparability assessment across laboratories. By providing accurate reference values for both parent vitamins and metabolites, these materials support a better understanding of the relationship between dietary intake and overall nutritional status.

Keywords:  25-hydroxyvitamin D3; cholecalciferol; ergocalciferol; vitamin D; vitamin D metabolites; vitamin D2; vitamin D3

DOI:  https://doi.org/10.1021/acs.jafc.6c01298
Anal Chim Acta. 2026 Jun 08. pii: S0003-2670(26)00344-2. [Epub ahead of print]1402 345394

Standardized ready-to-use natural deep eutectic solvent-impregnated polypropylene fiber units for robust and high-throughput determination of tyrosine kinase inhibitors in biological fluids.

Dong Wang, Mengrong Li, Xiangyu Zhang, Xu Miao, Lifeng Han, Di Chen.

   BACKGROUND: Therapeutic drug monitoring (TDM) of tyrosine kinase inhibitors (TKIs) is essential for individualized dosing due to their narrow therapeutic windows and pronounced pharmacokinetic variability. However, routine TDM is still hindered by sample preparation strategies that rely on labor-intensive workflows, high consumption of toxic organic solvents, and poor procedural standardization, limiting their suitability for high-throughput and green clinical analysis. Therefore, there is a clear need for a standardized, eco-friendly, and ready-to-use sample preparation strategy that enables robust and routine determination of TKIs in plasma.
RESULTS: Herein, a standardized, ready-to-use extraction device inspired by pharmaceutical blister packaging was developed for the determination of nine TKIs in human plasma. Hydrophobic natural deep eutectic solvent (NADES, menthol-thymol, 2:1) was pre-impregnated into polypropylene fiber (PPF) and sealed as individual consumable units, enabling a unit-supported liquid-phase microextraction (NADES-PPF-SLPME) strategy suitable for high-throughput operation. Density functional theory revealed that extraction was governed by synergistic hydrogen bonding and π-π stacking interactions between NADES and TKIs. Under Box-Behnken optimized conditions, the method exhibited wide linearity (R2 ≥ 0.990), low limits of quantification (0.2-1.0 ng/mL), satisfactory recoveries (86.64-110.30%), and acceptable precision (RSD <14.10%). The standardized units retained extraction capacity above 86.47% after three months of storage and enabled reliable quantification of TKIs in real clinical plasma samples.
SIGNIFICANCE: This work introduces a robust "prepare-in-advance, use-on-demand" NADES-based microextraction strategy that integrates standardization, operational robustness, high throughput, and green analytical chemistry. By eliminating on-site solvent preparation and minimizing solvent consumption, the proposed method offers an eco-friendly and operationally simple solution for routine clinical TDM of TKIs in plasma.

Keywords:  Liquid chromatography-tandem mass spectrometry (LC-MS/MS); Liquid-phase microextraction (LPME); Natural deep eutectic solvent (NADES); Polypropylene fiber (PPF); Therapeutic drug monitoring (TDM); Tyrosine kinase inhibitors (TKI)

DOI:  https://doi.org/10.1016/j.aca.2026.345394