bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2026–10–18
27 papers selected by
Sofia Costa, Matterworks



  1. Bioanalysis. 2026 Oct 13. 1-11
       AIM: A sensitive LC-MS/MS method was developed and validated for the estimation of DM1 fortified with trastuzumab in human serum.
    MATERIALS AND METHODS: Quantification was performed in positive mode with protein precipitation extraction using DM4 as an internal standard. Chromatographic separation was achieved using gradient elution and column ACE 5 C18, 100 mm × 4.6 mm. The mobile phase consisted of 0.1% formic acid in 1 mM ammonium formate in water and acetonitrile:methanol (50:50%, v/v) with a total run time of 8.0 min.
    RESULTS: The calibration curve was linear over the range of 0.5-100 ng/mL. Inter-day and intra-day accuracy and precision, matrix effect, and recovery were well within the acceptance criteria.
    CONCLUSION: A method to quantify free DM1 in human serum was fully validated, and the validated assay was successfully applied to determine the clinical pharmacokinetics of DM1 in HER2-positive patients.
    Keywords:  DM1; HER2; LC-MS/MS; Trastuzumab; method validation; pharmacokinetics
    DOI:  https://doi.org/10.1080/17576180.2026.2746946
  2. Methods Mol Biol. 2027 ;3071 3-16
      Mass Spectrometry Data Management System (MSDMS) is a comprehensive software solution for managing small molecule mass spectrometry (MS or MS/MS) libraries in MassBank format. Starting from large public libraries, MSDMS enables the creation of one or more custom libraries without having to run reference compounds or manage unknowns. Custom libraries improve the quality and speed of identification by LC-MS/MS screening of exogenous and endogenous compounds in complex biological samples. With a container-based architecture and Docker Compose configuration, MSDMS can be deployed as a website or as a local software application. Its use is explained in a stepwise manner and illustrated with human urine sample screening.
    Keywords:  Drug of abuse; Libraries; MS/MS; Mass spectrometry; MassBank; Metabolites
    DOI:  https://doi.org/10.1007/978-1-0716-5519-1_1
  3. Methods Mol Biol. 2027 ;3071 309-336
      We present a simple, practical workflow for annotating tandem mass spectrometry (MS/MS) data of small molecules using advanced machine learning and a reference library. The discovery and structural characterization of small molecules is central to biology, chemistry, and medicine. MS/MS has become the leading technology for this task, yet the majority of spectra from untargeted metabolomics remain unannotated, limiting our understanding of the underlying chemical diversity. Artificial intelligence (AI) is rapidly reshaping many areas of science, and mass spectrometry is no exception. In this chapter, we introduce a practical workflow for annotating MS/MS data using two complementary resources: DreaMS, a foundation model for mass spectrometry, and MassSpecGym, a large reference library and benchmarking platform. DreaMS embeds mass spectra into a representation space where structural similarity is preserved, and MassSpecGym provides anchor points for retrieving identical or related molecules. Together, they form an ecosystem that enables efficient annotation of experimental MS/MS data. We demonstrate this approach on alkaloid data from Piper fimbriulatum, showing how DreaMS can retrieve exact matches or place unannotated spectra alongside structurally related compounds. All steps are provided as easy-to-follow protocols, designed to run on standard hardware and requiring no modifications to existing metabolomics pipelines. Readers will learn how to integrate AI tools into their own workflows for compound annotation, molecular networking, and discovery. Overall, this chapter aims to empower biologists and chemists to harness machine learning for metabolomics, transforming unannotated spectra into interpretable chemical knowledge.
    Keywords:  Foundation model; Mass spectra embeddings; Mass spectrometry; Retrieval; benchmark
    DOI:  https://doi.org/10.1007/978-1-0716-5519-1_14
  4. Talanta. 2026 Oct 13. pii: S0039-9140(26)01426-8. [Epub ahead of print]313(Pt A): 130770
      Medicinal plants and fungi produce numerous structurally diverse metabolites, and many of these occur as isomers that are challenging to differentiate. Consequently, when mass spectrometry imaging (MSI) is used to spatially localize these compounds, annotation accuracy suffers from isobaric and isomeric interferences that accurate mass alone cannot resolve. To address this, we established an integrated spatial metabolomics strategy combining an optimized tape-assisted frozen section protocol, desorption electrospray ionization ion mobility mass spectrometry imaging (DESI-IM-MSI), and a cross-platform annotation workflow. The frozen section protocol was evaluated through blank control and repeated experiments, showing minimal background interference. In the annotation workflow, metabolites are first annotated in tissue extracts by liquid chromatography ion mobility mass spectrometry (LC-IM-MS), and then matched to DESI-IM-MSI images through shared drift time and m/z values. This enables orthogonal validation of metabolite annotations using retention time, drift time, and MS/MS fragmentation data. Applying this strategy to four plants (Ginkgo biloba, Panax ginseng, Scrophularia ningpoensis, and Salvia miltiorrhiza) and one fungus (Ganoderma lingzhi) enabled the first simultaneous imaging of multiple isomeric metabolites, including ginkgolide J and C, each resolved from its isomers. These isomers exhibited distinct tissue-specific distributions across these species. This strategy also reduced misannotations and resolved positional isomers, isobaric compounds, and background interferences that were indistinguishable by conventional MSI. This integrated workflow provides a practical approach for isomer-resolved spatial metabolomics across chemically complex plant and fungal matrices.
    Keywords:  DESI-IM-MSI; Ion mobility mass spectrometry; Isomer separation; Mass spectrometry imaging; Spatial metabolomics
    DOI:  https://doi.org/10.1016/j.talanta.2026.130770
  5. Anal Chim Acta. 2026 Nov 22. pii: S0003-2670(26)01181-5. [Epub ahead of print]1424 346231
       BACKGROUND: Statins are the most prescribed cholesterol-lowering drugs in the world. Reversed-phase ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry (RP-UHPLC/MS/MS) enables the analysis of isomeric lipid species, and the chemical derivatization enhances ionization efficiency. Here, we address the need for a validated quantitative method for sterols and tocopherols in human plasma and its application for the characterization of statin-induced alterations in lipid composition at the level of isomeric species.
    RESULTS: We developed a high-throughput RP-UHPLC/MS/MS method using multiple reaction monitoring (MRM) in the negative ion mode, which is based on the chemical derivatization with 3-(chlorosulfonyl)benzoic acid. The optimized and validated method using eight internal standards (IS) was applied to NIST SRM 1950, which enabled the quantification of 18 sterol species and two tocopherols (α- and γ-tocopherols). The lipidomic profiling of human plasma samples obtained from 41 statin-treated and 41 statin-naïve subjects provided a broad overview of cholesterol-related lipids. The separation of sterol isomers was an essential aspect due to the varying statistical importance of individual isomeric species.
    SIGNIFICANCE: This methodology provides a highly sensitive and selective quantitative analysis of free sterol species and tocopherols with isomeric structural resolution, which is critical for biological interpretation. Univariate and multivariate statistical analyses demonstrated statistically significant alterations in the statin-treated cohort among endogenous free sterol species and α-tocopherol, while exogenous free sterols showed no statistically significant changes.
    Keywords:  Derivatization; Human plasma; Lipidomics; Mass spectrometry; Reversed-phase liquid chromatography; Statins; Sterol lipids
    DOI:  https://doi.org/10.1016/j.aca.2026.346231
  6. Methods Mol Biol. 2027 ;3084 45-76
      Altered metabolism is a hallmark of cancer, where rewiring of cellular metabolic pathways is essential for tumor initiation, support of rapid proliferation, and adaptation to new metastatic sites. Metabolomics has emerged as a powerful tool to comprehensively characterize the metabolome of cancers and holds promise to transform understanding of how oncogenes can drive tumorigenesis and metastasis, identify cancer-specific metabolic dependencies, and provide novel therapeutic opportunities. This chapter describes methods to extract metabolites from Ewing sarcoma (EwS) cells grown in 2D or 3D cultures and from EwS mouse xenograft tissues, and to broadly analyze these compounds using an untargeted metabolite profiling approach. This methodology is likely applicable to a wide range of cultured cell and tissue types.
    Keywords:  Ewing sarcoma; Liquid chromatography mass spectrometry; Spheroids; Tumor; Untargeted metabolomics; Xenograft
    DOI:  https://doi.org/10.1007/978-1-0716-5587-0_4
  7. J Chromatogr B Analyt Technol Biomed Life Sci. 2026 Sep 28. pii: S1570-0232(26)00400-9. [Epub ahead of print]1285 125311
      Endogenous molecules are proposed as biomarkers to assess drug transporter function, with changes in their concentrations reflecting altered transporter activity. In this study, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed, comprising a hydrophilic interaction liquid chromatography (HILIC) method and a reversed-phase liquid chromatography (RPLC) method both with MS/MS, using a single supernatant to quantify plasma biomarkers of clinically relevant drug transporters: coproporphyrin I (CPI), 4-pyridoxic acid (PDA), N1-methylnicotinamide (NMN), and 1-methyladenosine (m1A). Optimization resulted in a 5-min HILIC method for PDA, NMN, and m1A using a pH 9 mobile phase containing 10 mM ammonium acetate and 0.04% ammonium hydroxide to achieve acceptable peak shapes and retention, with 5% methanol added to the organic phase to maintain salt solubility. For CPI and CPIII, a 3.5-min RPLC method at pH 2.7 enabled baseline separation of the two isomers with a low gradient steepness of 0.032 at 60 °C. Protein precipitation provided lower limits of quantification of 0.18-4.00 ng/mL across the different biomarkers, while parallelism experiments confirmed 3 × charcoal-stripped K2EDTA human plasma as a suitable surrogate matrix. Fit-for-purpose validation demonstrated intra- and inter-assay accuracy and precision and confirmed assay selectivity. The final method was applied to plasma samples from healthy volunteers, resulting in a geomean of the baseline levels of 0.52 ng/mL for CPI, 5.5 ng/mL for PDA, 14.7 ng/mL for NMN, and 28.9 ng/mL for m1A, consistent with previously published data. The variation in the baseline levels was mainly described by sex for CPI and by the sex-age interaction for PDA.
    Keywords:  1-Methyladenosine; 4-Pyridoxic acid; Coproporphyrin; HILIC; N1-methylnicotinamide; RPLC; Transporter biomarkers
    DOI:  https://doi.org/10.1016/j.jchromb.2026.125311
  8. J Chromatogr A. 2026 Oct 03. pii: S0021-9673(26)00841-1. [Epub ahead of print]1789 467515
      Water-soluble flavor precursors (WSFPs) in sheep meat are key foundational substances that confer its unique and intense flavor. This study established an efficient analytical method for the simultaneous quantification of 34 WSFPs in sheep meat by combining streamlined sample preparation with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Sheep meat samples were homogenized in water, followed by cleanup using dispersive solid-phase extraction (d-SPE), and subsequently analyzed by LC-MS/MS. Separation was achieved on a BEH Amide column (2.1 mm × 100 mm, 1.7 μm) with a gradient elution of ammonium formate aqueous solution and acetonitrile solution as the mobile phase. Detection was performed in electrospray ionization (ESI) mode with positive/negative ion switching and multiple reaction monitoring (MRM). Isotope-labeled internal standards were employed for quantification. The 34 analytes, spanning five chemical classes - 24 amino acids, 2 nucleotides, 3 reducing sugars, 4 small peptides, and 1 vitamin B1 (thiamine) - were successfully quantified. The method exhibited excellent linearity (R² ≥ 0.9909), with quantification limits ranging from 0.01 to 5 mg/kg, average spike recovery rates of 80.1%-109%, and relative standard deviations (RSD) below 9.9%. The developed method was validated using real sheep meat samples and demonstrated to be simple, accurate, reliable, and suitable for the simultaneous quantification of these 34 WSFPs. Furthermore, it proved applicable for monitoring changes in WSFP content during sheep meat storage.
    Keywords:  Dispersed solid-phase extraction; LC-MS/MS; Sheep meat; Simultaneous determination; Water-soluble flavor precursors
    DOI:  https://doi.org/10.1016/j.chroma.2026.467515
  9. J Chromatogr B Analyt Technol Biomed Life Sci. 2026 Oct 10. pii: S1570-0232(26)00417-4. [Epub ahead of print]1285 125328
      This study presents the development and validation of a one-step extraction method coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the simultaneous analysis of 100 compounds in human hair. Specifically, the method can detect a broad range of drugs in human hair, including analgesics, antidepressants, antipsychotics, benzodiazepines, classic drugs of abuse (DOA) and novel psychoactive substances (NPS). The drugs were extracted from 20 mg of washed hair by incubation for 3 h in a mixture of 1 mL of 0.1 M HCl in methanol. Analytical performance was evaluated in terms of linearity, sensitivity, accuracy, precision, matrix effects and recovery. The developed method demonstrated high sensitivity (the limits of detection (LOD) ranged from 1.25 to 150 pg/mg and the quantitation limit (LOQ) ranged from 3.75 to 450 pg/mg), accuracy and precision were within acceptable limits. The matrix effect expressed as ion suppression/enhancement of each analyte was in the range ± 25% for all analytes. Post-preparative stability of analytes was higher than 85%, while no carryover between runs was observed. Application to authentic hair samples confirmed its potential to detect a wide range of drugs and metabolites and to reveal patterns of drug use. Overall, the method offers a practical and efficient tool for comprehensive hair analysis, well suited for routine forensic and clinical toxicology in the context of increasing polydrug exposure.
    Keywords:  Drugs of abuse; Hair analysis; LC-MS/MS; Long-term exposure; Method validation; Multi-analyte method; Pharmaceuticals
    DOI:  https://doi.org/10.1016/j.jchromb.2026.125328
  10. Molecules. 2026 Sep 24. pii: 3406. [Epub ahead of print]31(19):
      A robust liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed and validated for determining erythromycin A (ERY A) and its metabolites: erythromycin B (ERY B), erythromycin C (ERY C), erythromycin A N-oxide (ENO), anhydroerythromycin A (AHEA), N-demethylerythromycin A (NDEA), erythromycin A enol ether (EAEE), and pseudoerythromycin A enol ether (PSEE) in salmon muscle with skin. Tissue samples (1.00 g) fortified with ERY A, ERY B, ERY C, ENO, EAEE, and PSEE at 50-200 ng/g and AHEA and NDEA at 500-2000 ng/g, using a surrogate internal standard, were extracted with acetonitrile, defatted hexane, and diluted water, resulting in accuracy from 87% to 108%, precision from 3% to 13%, and estimated LOQ from 0.02 to 1.2 ng/g. Incurred salmon showed ERY A as the major residue at 3 days post-administration and NDEA and AHEA as potential markers exceeding the 500 ng/g level on Day 28.
    Keywords:  Atlantic salmon; LC–MS/MS; analytical quantitation; antibiotics; erythromycin A; erythromycin metabolites; veterinary drug residues
    DOI:  https://doi.org/10.3390/molecules31193406
  11. Foods. 2026 Sep 28. pii: 3465. [Epub ahead of print]15(19):
      To enable rapid and accurate determination of sulfonamide residues in animal-derived foods, a method was developed for the simultaneous analysis of 20 sulfonamides by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) combined with a FaVEx one-step cleanup column, using pork as a representative matrix. After extraction, samples were rapidly purified with a FaVEx-NM column and analysed in multiple reaction monitoring mode. Matrix-matched calibration was employed to compensate for matrix effects. The method showed good linearity for all analytes within their respective concentration ranges, with correlation coefficients (R2) of 0.9922-0.9998. The limits of detection and quantification were 0.05-0.74 μg/kg and 0.09-1.48 μg/kg, respectively, indicating high sensitivity. At spiking levels of 1, 3, and 5 μg/kg, mean recoveries ranged from 70.95% to 112.20%, with relative standard deviations below 11%, demonstrating satisfactory accuracy and precision. The proposed method is simple, efficient, sensitive, and reproducible, and is suitable for rapid screening and quantitative determination of multiple sulfonamide residues in pork, providing reliable technical support for residue monitoring in animal-derived foods.
    Keywords:  FaVEx; UHPLC–MS/MS; method validation; one-step purification column; pork; residue analysis
    DOI:  https://doi.org/10.3390/foods15193465
  12. J Mass Spectrom. 2026 Nov;61(11): e70119
      Screening of major cannabinoids in cannabis-derived extracts is needed when these extracts are applied in pharmacological and biological studies. Precursor ion scan-mass spectrometry (PIS-MS) is a viable approach for the detection and screening of major cannabinoids through characteristic MS/MS fragmentation behavior. A PIS-MS method was developed utilizing electrospray ionization (ESI) operated in the positive ion mode on a triple quadrupole-linear ion trap mass spectrometer (QTRAP 6500). Three cannabis extracts were screened based on established MS/MS fragmentation pattern. Characteristic product ions at m/z 193.1 and 233.1 were optimized for PIS-MS analysis. In addition, tandem mass spectrometry (MS/MS) was performed to aid in the putative identification of unknown cannabinoids, whereas authentic standards were used, when available, to confirm the identity. A quadrupole-Orbitrap (Exploris 240) mass spectrometer equipped with ESI was also utilized to provide accurate mass measurements for single-stage and MS/MS analyses, supporting the proposed structures of cannabinoids and their product ions. PIS-MS complemented with high-resolution mass spectrometry (HRMS) analysis revealed the existence of six major cannabinoids in two plant extracts, and nine in the third one. Among the detected phytocannabinoids, an unexpected cannabinoid, namely, sesquicannabigerol (Sesqui-CBG), was also identified among the most abundant ones. The MS/MS fragmentation behavior in both positive and negative ionization for Sesqui-CBG was established for the first time, supported by accurate mass measurements and second-generation MS/MS (MS3) experiments. In conclusion, PIS-MS provided an effective approach for the screening of abundant cannabinoids in plant products intended for therapeutic applications. MS/MS and accurate mass measurements confirmed the putative identification of detected cannabinoids. A comprehensive study for Sesqui-CBG was performed, elucidating its fragmentation pathways and product ions.
    DOI:  https://doi.org/10.1002/jms.70119
  13. J Pharm Biomed Anal. 2026 Oct 12. pii: S0731-7085(26)00430-9. [Epub ahead of print]283 117762
      An automated protein precipitation (PPT) method coupled with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed using an in-house developed automatic sample pretreatment platform. The platform integrates six sets of 8-position tube racks, a centrifuge vials rack, a reagent rack, an automatic decapper, a vortex mixer, a centrifuge, and an X-Y-Z axis robotic arm. The online sample preparation workflows and chromatographic conditions were systematically optimized for the comprehensive analysis of 19 nitazene analogues in human urine. The robotic platform operates in a pipeline-parallel processing mode, in which UPLC-MS/MS analysis (18 min per sample) is performed for one batch, while the subsequent batch of eight samples undergoes automated pretreatment (30 min per batch) without manual intervention. This design achieves a total turnaround time of 14.9 h for 48 samples, corresponding to an average processing time of 18.6 min per sample. Furthermore, the entire pretreatment procedure consumes only 400 μL of methanol per sample, thereby reducing organic solvent consumption. The method demonstrated good precision, with intra-day relative standard deviations (RSDs) of 1.2-7.0% and inter-day RSDs of 0.6-5.1%, indicating satisfactory analytical reproducibility. Application of the method to 24 authentic urine samples identified 15 positives specimens, with N,N-dimethylamino etonitazene (0.4-168.5 ng/mL) being the most frequently detected analyte, together with three other nitazene analogues or metabolites. Overall, the developed automated PPT-UPLC-MS/MS platform provides a rapid, reproducible, and solvent-efficient approach for high-throughput screening of nitazene analogues in human urine, with potential applications in forensic toxicology and public health surveillance.
    Keywords:  Automated sample preparation; Nitazene analogues; Robotic arm; UPLC-MS/MS; Urine analysis
    DOI:  https://doi.org/10.1016/j.jpba.2026.117762
  14. J Chromatogr B Analyt Technol Biomed Life Sci. 2026 Oct 11. pii: S1570-0232(26)00426-5. [Epub ahead of print]1285 125337
      A practical and robust sample preparation method was developed for the simultaneous quantification of 34 per- and polyfluoroalkyl substances (PFAS) in complex liver matrices by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Cat (Felis silvestris catus) liver was used as the primary matrix for method optimization and validation. The final proposed method (Procedure 6), selected through systematic evaluation, consisted of alkaline digestion of 0.1 g freeze-dried tissue, hexane washing, and dual solid-phase extraction cleanup using Captiva EMR Food II and Strata PFAS cartridges. Procedure 6 achieved internal standard-corrected recoveries within 70-120% for almost all analytes, except for branched MeFOSAA (130%) and PFMBA (130%), although absolute recoveries for some PFAS were below 50%. The mean matrix effect was 12%, with individual values ranging from -43% to 49% (excluding FTSAs), indicating effective mitigation of ion suppression and enhancement. Both intra-batch and inter-batch coefficients of variation were below 15%, and method detection limits ranged from 0.0091 to 0.55 ng g-1 dry weight for all target PFAS and from 0.013 to 0.35 ng g-1 dry weight for major PFCAs and PFSAs. Applicability was further evaluated using common cormorant (Phalacrocorax carbo) liver and cat kidney and muscle samples, confirming reliable quantification across tissues with different matrix compositions and PFAS concentration ranges. Overall, the proposed method enables sensitive and reliable quantification of structurally diverse legacy and alternative/emerging PFAS in complex biological tissues using only 0.1 g of dry tissue.
    Keywords:  LC–MS/MS; Liver; Matrix effects; PFAS; Sample preparation; Wildlife
    DOI:  https://doi.org/10.1016/j.jchromb.2026.125337
  15. Methods Mol Biol. 2027 ;3071 29-54
      We present the Spectra software, an R/Bioconductor package, defining an efficient infrastructure for storing, handling, and visualizing mass spectrometry data. We describe how Spectra adapts to different data types, sizes, and use cases, addressing scalability while keeping a consistent user interface. We also demonstrate how it can integrate with third-party Python tools and follow modern tidyomics principles, seamlessly integrating with more general tidy data science tools.
    Keywords:  Bioconductor; Mass spectrometry; Metabolomics; Proteomics; R; Reproducible research; Software
    DOI:  https://doi.org/10.1007/978-1-0716-5519-1_3
  16. Anal Chim Acta. 2026 Nov 22. pii: S0003-2670(26)01187-6. [Epub ahead of print]1424 346237
       BACKGROUND: In metabolomics studies, biological data are highly complex, requiring robust computational tools to detect biological variation in the organism under investigation. Despite this, comparative studies of data processing software for GC-MS data are scarce. This work evaluated the performance of two open-source software programs, XCMS and MS-DIAL, on three datasets: cells, serum, and tissue, acquired by GC-MS.
    RESULTS: Software performance was assessed based on the quality of the raw data matrix, the number of extracted features, the presence of missing values, and the number of annotated metabolites or chemical classes. Overall, both tools produced robust matrices and adequate statistical models, with high similarity in the regulation of common metabolites. For the investigated datasets, XCMS demonstrated slightly better performance in raw matrix quality, while MS-DIAL showed a higher correlation with the annotations. The combination of matrices broadened metabolic coverage, allowing for improvements in supervised statistical models. The choice of data processing platform and the parameters used directly impact the extracted data matrix and the conclusions regarding metabolic alterations.
    SIGNIFICANCE: These observations reinforce the need for careful evaluation in metabolomics analyses, so that selection involves not only parameters such as the number of features and metabolites obtained, but also the method's stability and its ability to show the chemical variability of the analyzed biological system.
    Keywords:  Bioinformatics; Data processing; MS-DIAL; Metabolite annotation; Metabolomics; Peak detection; XCMS
    DOI:  https://doi.org/10.1016/j.aca.2026.346237
  17. Int J Mol Sci. 2026 Oct 04. pii: 8852. [Epub ahead of print]27(19):
      Herein, an automated, parameter-based workflow is introduced for processing time-resolved high-resolution mass spectrometry (HRMS) data. Its utility is demonstrated using the reaction between the ABTS•+ radical cation and the polyphenolic antioxidant naringenin. Data were collected using HRMS coupled to high-performance liquid chromatography (HPLC) in negative ion mode. The algorithm compares sequential time-resolved HRMS measurements to generate kinetic curves and calculate parameters for every detected species. Based on these curves and parameters, we can tentatively classify each species as a reagent, intermediate, or product. The algorithm was implemented as Java-based software. As a result, extensive data arrays of 1.3 million m/z-intensity pairs per experimental series were processed automatically. The workflow generated manageable candidate sets in each replicate series. Cross-replicate matching using a 5 ppm mass tolerance retained 29 ion tracks consistently detected in all three reaction runs for subsequent analysis. These ions can then be examined manually to identify compound structures. Overall, the approach provides a screening tool for untargeted reaction monitoring and supports subsequent structural annotation in complex chemical systems.
    Keywords:  LC–HRMS; high-resolution mass spectrometry; ion prioritization; reaction monitoring; time-resolved analysis; untargeted analysis
    DOI:  https://doi.org/10.3390/ijms27198852
  18. Metabolomics. 2026 Oct 17. pii: 172. [Epub ahead of print]22(6):
       INTRODUCTION: Machine learning models trained on metabolomics data frequently show reduced performance when applied to independent cohorts because of domain shifts introduced by differences in analytical platforms, sample handling, storage conditions, and metabolite quantification procedures. Robust approaches for harmonizing metabolomics datasets across cohorts are therefore needed to improve model transferability and reproducibility.
    OBJECTIVES: To evaluate the impact of matched samples on domain harmonization and cross-cohort prediction performance in NMR metabolomics data, and to compare multiple harmonization strategies for improving model generalization across independently acquired datasets.
    METHODS: A machine-learning framework was developed to classify ICD-10 code I50.9 (unspecified heart failure) using plasma NMR metabolomics data from the Estonian Biobank. Models were trained on a source dataset comprising 12,000 samples measured at Nightingale Health and evaluated on an independently measured destination dataset of 295 samples acquired on a different NMR platform. Harmonization approaches included within-domain normalization, Optimal Transport, Bridge mapping, and Empirical Bayes correction. The effect of matched samples was assessed using up to 108 duplicated biospecimens measured in both datasets. Additional validation was performed using independently generated human gestational diabetes and mouse diabetes metabolomics datasets from Metabolomics Workbench.
    RESULTS: Domain harmonization generally improved cross-cohort prediction compared with unaligned data, particularly when matched samples were available. Predictive performance increased as the number of matched samples used for calibration increased, although gains varied across methods. Nevertheless, simple within-domain normalization consistently provided strong performance and often matched or exceeded more complex alignment approaches. External validation using fully unmatched human and mouse metabolomics datasets demonstrated that harmonization strategies improved classification performance relative to raw data, supporting the broader applicability of the framework.
    CONCLUSION: Matched samples substantially enhance domain harmonization and improve the transferability of metabolomics prediction models across analytical platforms and cohorts. However, robust normalization remains a strong baseline, and the benefits of more sophisticated alignment methods depend on the availability and representativeness of matched reference samples. These findings provide practical guidance for developing reproducible cross-cohort metabolomics machine-learning models while preserving biologically relevant signals.
    Keywords:  Cardiovascular disease; Cross-cohort; Data transformation; Domain alignment; Independent dataset; Machine learning; Matched samples; Metabolomics; NMR
    DOI:  https://doi.org/10.1007/s11306-026-02543-0
  19. Anal Chim Acta. 2026 Nov 22. pii: S0003-2670(26)01189-X. [Epub ahead of print]1424 346239
       BACKGROUND: Dammarane-type ginsenosides (DTGs) exhibit extensive isomerism including aglycone isomers, glycosylation site isomers, double-bond positional isomers, and R/S configurational isomers. Many of these isomers co-elute in liquid chromatography and are difficult to distinguish by MS/MS alone, compromising the accuracy of identification in Panax ginseng extract. Consequently, a more systematic approach is needed to separate and identify these isomers.
    RESULTS: Multi-pass cyclic ion mobility (cIMS) was validated on both reference standards and Panax ginseng extracts for its ability to resolve challenging DTG isomers. Following optimization of the trap collision energy, a systematic putative identification strategy was established by integrating MS/MS data, CCS values of intact DTGs, and CCS values of their characteristic aglycone fragments. This approach enables the differentiation of aglycone isomers, sugar type isomers, glycosidic linkage isomers, glycosylation site isomers, R/S configurational isomers and double-bond positional isomers, markedly improving the reliability of identification.
    SIGNIFICANCE: The use of characteristic CCS values of homologous aglycones offers a complementary approach for inferring C-20 R/S configurations, which may help to address a key limitation of conventional MS in certain cases. While the current study focuses on ginsenosides, this workflow-particularly the integration of MS/MS with aglycone CCS data-may serve as a useful reference for isomer identification in other natural products with similar isomeric complexity.
    Keywords:  Collision cross section; Cyclic ion mobility; Dammarane-type ginsenoside; Isomer identification; Mass spectrometry
    DOI:  https://doi.org/10.1016/j.aca.2026.346239
  20. Talanta. 2026 Oct 12. pii: S0039-9140(26)01425-6. [Epub ahead of print]313(Pt A): 130769
      Perfluoroalkyl and polyfluoroalkyl substances (PFAS) are persistent organic contaminants of global concern. In response to increasingly stringent international regulations, including the addition of long-chain perfluoroalkyl carboxylic acids (LC-PFCA) to the Stockholm Convention in 2025, accurate monitoring of these compounds in food matrices is essential for assessing human exposure. Although analytical methods for PFAS in drinking water are well established, reliable quantification of LC-PFAS in foods remains challenging because of matrix complexity, strong adsorption of long-chain compounds, and the limited availability of suitable isotope-labeled internal standards. Here, we report a robust and traceable strategy for the accurate quantification of LC-PFAS (C ≥ 10) in food matrices. Building on a comprehensive PFAS measurement framework covering homologues from C4 to C18, we addressed key analytical limitations by introducing an 18O-labeling approach for carboxylic acid compounds to compensate for gaps in commercially available internal standards. The isotopic purity and stability of the labeled compounds were systematically validated. In addition, a liquid-liquid extraction procedure combined with C8 reversed-phase chromatography minimized analyte loss resulting from strong hydrophobic adsorption, enabling accurate, precise, and sensitive determination of LC-PFAS. This method provides a practical, cost-effective, and reliable analytical approach for routine LC-MS/MS analysis and supports improved food monitoring and long-term exposure assessment.
    Keywords:  Food matrices; LC-MS/MS; Liquid–liquid extraction; Long-chain perfluorocarboxylic acids; Preparative stable isotope labeling with (18)O-water; per- and polyfluoroalkyl substances
    DOI:  https://doi.org/10.1016/j.talanta.2026.130769
  21. Environ Monit Assess. 2026 Oct 16. pii: 1208. [Epub ahead of print]198(11):
      Per- and polyfluoroalkyl substances (PFAS) are widely used in consumer products, raising health and environmental concerns due to their potential for toxicity and bioaccumulation. Although methods for PFAS extraction and analysis exist, few are tailored for consumer products, and most rely on time-consuming and costly solid-phase extraction (SPE). This study introduces a new SPE-free method for extracting and analyzing PFAS in six consumer product categories: paper, plastics, fabrics, cosmetics, metals, and "other". The method applies co-solvation extraction, large-volume injection, and co-injection of 0.1% acetic acid, significantly enhancing detection limits and PFAS peak shapes. Recoveries of surrogate standards in plastics and metals met quality control criteria (50-150%). However, paper, fabric, cosmetic, and "other" matrices adversely affected the recoveries of fluorotelomer sulfonic acids and electrochemical fluorination-derived PFAS surrogates. Recoveries of native PFAS spikes in polymer containers and aluminum foil ranged from 82 to 140%, except for 3:3 FTCA and 8:2 diPAP. Meanwhile, more complex matrices including, cosmetic pressed powder, food packaging, athletic tape, and dress shirt, substantially impacted the recoveries of multiple spiked PFAS. Among the extraction methods evaluated, Soxhlet extraction yielded the highest PFAS concentrations but was prone to matrix interference and potential PFAS artifacts, limiting its suitability for PFAS analysis. In contrast, cryo-milling enhanced PFAS extraction when incorporated into the co-solvation protocol. Overall, the co-solvation method provides a complementary approach for PFAS analysis in selected consumer products, although further optimization is needed to improve the recovery of challenging analytes and minimize matrix interferences in complex matrices.
    Keywords:  Co-solvation extraction; Consumer products; Liquid chromatography tandem mass spectrometry (LC/MS/MS); Per- and polyfluoroalkyl substances (PFAS)
    DOI:  https://doi.org/10.1007/s10661-026-16031-4
  22. Crit Rev Anal Chem. 2026 Oct 14. 1-27
      Molecular imaging technologies have transformed analytical chemistry by enabling molecular identification and spatial localization within intact biological specimens. Advances in mass spectrometry imaging (MSI), Raman imaging, imaging mass cytometry (IMC), and emerging spatial analytical platforms have expanded the investigation of tissue heterogeneity and molecular organization. However, quantitative reliability, reproducibility, standardization, computational complexity, and clinical translation remain significant challenges. This review critically evaluates the analytical performance of current molecular imaging technologies, emphasizing spatial resolution, sensitivity, molecular coverage, quantitative capability, multiplexing, reproducibility, computational integration, artificial intelligence (AI)-assisted analysis, and clinical readiness. No single modality simultaneously provides optimal spatial resolution, molecular coverage, quantitative accuracy, throughput, and reproducibility. MSI enables comprehensive molecular profiling, Raman imaging provides label-free chemical specificity, IMC supports highly multiplexed protein analysis, and emerging spatial omics platforms offer systems-level biological insights. Nevertheless, matrix effects, workflow variability, computational demands, limited standardization, and insufficient multicenter validation restrict broader analytical and clinical implementation. AI-assisted analysis and multimodal data integration offer opportunities to improve performance but require transparent validation and harmonized workflows. Future progress will depend on standardized analytical protocols, quantitative validation, explainable AI, multimodal integration, automated quality control, and international harmonization to establish molecular imaging as robust, reproducible, and clinically translatable analytical platforms.
    Keywords:  Imaging mass cytometry; Raman imaging; mass spectrometry imaging; molecular imaging; spatial omics
    DOI:  https://doi.org/10.1080/10408347.2026.2742470
  23. J Cheminform. 2026 Aug 10. pii: 142. [Epub ahead of print]18(1):
      Reliable quality control of mass spectrometry data remains a major bottleneck in target, suspect and non-target screening workflows. In non-target analysis, thousands of features can be extracted through automated peak picking, many of which require manual verification to exclude artefacts arising from noise, co-elution, inconsistent chromatographic behavior or statistical prioritization. Similarly, suspect screening workflows depend on effective chromatographic and spectral quality control to support confidence in annotated features. However, existing quality control practices are often fragmented across vendor software and custom scripts, limiting reproducibility and scalability. This article describes pyMSscreen, a unified framework that enables automated and reproducible chromatographic quality control across target, suspect, and non-target mass spectrometry workflows. The backend leverages RDKit and pyOpenMS for compound validation and spectral extraction, while the frontend provides a web-based interface for systematic inspection of chromatograms and mass spectra. The development of pyMSscreen draws on experience gained from the earlier R-based Shinyscreen, which showed that accessible graphical user interface can greatly simplify the review of liquid chromatography mass spectrometry data. However, the practical limitations of the Shiny framework, including difficulties with deployment, motivated the creation of a more flexible and modern solution. pyMSscreen employs a modular architecture that supports target, suspect, and non-target screening by accommodating both SMILES or m/z only input lists. Automated quality control metrics are applied consistently across workflows, enabling assessment of peak shape, signal intensity, retention-time alignment, and background noise prior to downstream interpretation. Container-based deployment ensures reproducible installation and execution across computational environments. The performance and applicability of pyMSscreen is illustrated using a representative non-target dataset and suspect screening workflow demonstrating consistent results relative to established approaches, while substantially reducing manual data handling and review time. Overall, pyMSscreen provides an efficient, transparent, and reproducible platform for chromatographic quality control and data curation in high resolution mass spectrometry based cheminformatics workflows. The code is openly available (Artistic 2.0 license) at https://gitlab.com/uniluxembourg/lcsb/eci/pymsscreen .Scientific contributionpyMSscreen presents a unified framework for chromatographic quality control that integrates automated quality metrics with interactive visual inspection of mass spectrometry data. The central contribution is the consistent evaluation of chromatographic peak quality and spectral alignment across target, suspect, and non-target screening workflows within a single methodology. This work builds on earlier developments in interactive mass spectrometry data review while establishing a scalable and reproducible approach to feature-level quality control.
    Keywords:  Docker; High resolution mass spectrometry; Interactive visualisation; Non-target screening; Open source software; Quality control; Spectral data analysis
    DOI:  https://doi.org/10.1186/s13321-026-01260-z
  24. J Chromatogr A. 2026 Oct 09. pii: S0021-9673(26)00864-2. [Epub ahead of print]1789 467538
      The complete characterization of food samples is often hampered by the polarity range of their constituents. Although comprehensive two-dimensional liquid chromatography (LC × LC) offers an enhanced separation space compared to one-dimensional LC, a single pair of columns is often unable to retain compounds across this entire range, leaving part of the separation space unused. In this work, an online multi-two-dimensional (2D) LC × LC method was developed to extend the separation space achievable with LC × LC, using tamarind (Tamarindus indica L.) pericarp as a chemically diverse model sample. An orthogonality study, screening nine reversed-phase liquid chromatography (RPLC) and hydrophilic liquid interaction chromatography (HILIC) columns under various mobile-phase conditions, was used to select the most promising conditions. A HILIC × RPLC method was able to separate moderately polar constituents well, however, leaving the most polar compounds poorly retained in the second dimension. A second, HILIC-based second-dimension method was therefore developed for this polar fraction. Both second-dimension columns were combined in a single analysis through a zero-flow column-switching strategy, allowing each column to be operated under its optimal conditions. The multi-2D configuration increased the fraction surface coverage from 0.507 to 0.533 for the individual LC × LC methods to 0.868, and yielded the highest effective peak capacity (339).
    Keywords:  Column screening; Multi-(2)D LC × LC; Orthogonality; Peak capacity; Tamarind
    DOI:  https://doi.org/10.1016/j.chroma.2026.467538
  25. Talanta. 2026 Oct 07. pii: S0039-9140(26)01400-1. [Epub ahead of print]313(Pt A): 130744
      Primary aldosteronism (PA) requires accurate subtype differentiation to guide targeted treatment. Urinary steroid profiling by liquid chromatography-tandem mass spectrometry (LC-MS/MS) offers a promising noninvasive strategy, but the clinical implementation of urinary steroid profiling remains constrained by manual hydrolysis and labor-intensive sample preparation. Here, we developed an automated magnetic-bead-assisted sequential extraction (MBASE) workflow that integrates thermally controlled enzymatic hydrolysis and WCX-based magnetic bead cleanup for simultaneous quantification of urinary aldosterone (ALD), tetrahydroaldosterone (THALD), 18-hydroxycorticosterone (18-OHB), 18-hydroxycortisol (18-OHF), and 18-oxocortisol (18-OXOF). The optimized WCX-MBASE procedure provided balanced extraction and selective cleanup for urinary aldosterone-pathway steroids, while the F5 column enabled effective chromatographic separation of the target analytes from selected endogenous and exogenous interferences. In this programmable workflow, urine hydrolysis (60 min) and extraction were completed in a single automated pretreatment sequence, reducing intermediate handling and manual intervention. The method showed recoveries of 87.14%-109.56%, within-run imprecision of 3.33%-11.53% and total imprecision of 3.86%-12.73%. Compared with the conventional workflow, MBASE completed the automated hydrolysis-extraction cycle within 76 min, and lowered pretreatment cost while maintaining high analytical concordance. Clinical application in 136 hypertensive patients, including 38 with unilateral primary aldosteronism (UPA), 38 with bilateral primary aldosteronism (BPA), and 60 with essential hypertension, showed increased urinary ALD and related steroids in PA. The combined five-steroid panel achieved an apparent AUC of 0.855 for UPA identification, with an optimism-corrected AUC of 0.827 after bootstrap internal validation. This enzymatic hydrolysis-MBASE workflow provides an automation-compatible LC-MS/MS strategy for rapid and reliable profiling of urinary aldosterone-pathway steroids, supporting further evaluation of its potential for noninvasive PA subtype assessment and treatment monitoring.
    Keywords:  Aldosterone-pathway steroids; Automation; LC-MS/MS; MBASE; Primary aldosteronism; Urine
    DOI:  https://doi.org/10.1016/j.talanta.2026.130744
  26. Anal Bioanal Chem. 2026 Oct 16.
      In 2011, the National Institute of Standards and Technology (NIST), in collaboration with the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) at the National Institutes of Health (NIH), issued Standard Reference Material (SRM)® 1950 Metabolites in Frozen Human Plasma to support metabolomics measurements. This critical review traces the development of SRM 1950 and assesses its use and impact over the past 15 years. To evaluate its impact, we reviewed more than 400 technical papers demonstrating its broad adoption in analytical, metabolomic, and lipidomic research. While SRM 1950 included certified values for selected amino acids, fatty acids, and clinical markers (such as cholesterol, glucose, 25-hydroxyvitamin D, and steroid hormones), its greatest impact has been as a shared material for interlaboratory comparisons and the community-generated consensus or target values established for the broad scope of compounds commonly measured in metabolomic and lipidomic studies. Many studies used SRM 1950 to validate analytical methods against NIST-certified values, while over 50 papers provided extensive qualitative and quantitative characterization and compared their results with interlaboratory consensus values and other studies to assess method and platform performance. The success of SRM 1950 helped to catalyze the development of additional NIST reference materials (RMs) for the "omics" communities and highlighted the potential of existing clinical and environmental matrix SRMs for further untargeted characterization and community reporting. Based on this literature review, we offer recommendations to expand the use and impact of the next generation of SRM 1950 and other SRMs/RMs intended and/or useful for untargeted analyses.
    Keywords:  Certified reference materials (CRMs); Lipidomics; Metabolomics; Quantification; Standard Reference Materials (SRMs); Untargeted analysis
    DOI:  https://doi.org/10.1007/s00216-026-06867-7
  27. Phytochem Anal. 2026 Oct 14.
       INTRODUCTION: In-depth profiling of plant-derived metabolites is essential for unraveling chemically diverse group of bioactive compounds that play essential roles in plant defense, adaptation, ecological interactions, and human health. Comprehensive profiling of these metabolites is important for understanding their biochemical diversity and exploring their pharmaceutical, agricultural, and industrial potentials. Metabolomics is an emerging platform for qualitative and quantitative assessment of metabolites, employing GC-MS, LC-MS, and NMR.
    OBJECTIVE: To compare and critically assess the extraction, data acquisition, and data-processing protocols including chemometric analysis and applications of metabolomics.
    METHODOLOGY: Metabolomics studies largely depend on optimized sample collection, extraction procedures, analytical platforms, and data-processing workflows for the chemical profiling of plant-derived metabolites. Following metabolite extraction from different plant parts, analytical data generated by GC-MS, LC-MS, and NMR are further analyzed, employing chemometric statistical approaches for identification of metabolic signatures, classification of plant samples, and to reveal biochemical variations associated with genetic and environmental factors.
    RESULTS: This review focuses on several applications of metabolomics in plant sciences, including elucidating plant responses to abiotic and biotic stresses, evaluating the effects of nutrient availability on metabolite biosynthesis, investigating genetic and phenotypic diversity among wild-type, cultivated, and transgenic plants, supporting crop improvement and metabolic engineering, authenticating medicinal plants, ensuring quality control, and accelerating the discovery of bioactive natural products.
    CONCLUSION: This review provides comprehensive comparison of various extraction and characterization techniques of secondary metabolites, which will provide valuable insights as well as further directions to researchers working in allied field.
    Keywords:  GC–MS; LC–MS; NMR spectroscopy; hierarchical clustering analysis; metabolite extraction; metabolomics; partial least squares‐discriminant analysis; principal component analysis
    DOI:  https://doi.org/10.1002/pca.70093