bims-metlip 2026-07-19 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2026–07–19
23 papers selected by
Sofia Costa, Matterworks

[Detection of Chlormezanone in Blood Using HPLC-MS/MS Method].
Development and Optimization of an LC-MS/MS Method for Quantification of Phosphatidylethanol in Human Whole Blood.
Development and validation of a multi-matrix LC-MS/MS method for quantification of 20 drugs in human postmortem and porcine surrogate matrices.
Authentic Spatial Metabolomics by Avoiding Hidden Pitfalls in MSI Workflows.
aiSysMet: AI-Powered Systems Metabolomics for Biomarker Discovery.
Mass Spectrometry as a Tool for Metabolomics in Cancer.
Improving detection of low-abundant pharmaceuticals and neurotransmitters via quadrupole isolation in MALDI mass spectrometry imaging.
Quantification of catecholamines in human plasma using isotope dilution mass spectrometry with para-aminobenzoic acid-modified magnetic polydopa particles.
Validation of an UHPLC-MS/MS Assay for the Quantification of Isoniazid and Four Major Metabolites in Human Plasma.
Structure-Based Comparative Metabolomics Identifies LysoPE 15:0 as a Candidate Metabolite Marker of Influenza Virus Infection Dynamics.
A Metrologically Traceable Candidate Reference Measurement Procedure (cRMP) for Dehydroepiandrosterone Sulfate in Human Serum Based on Isotope Dilution-Liquid Chromatography-Tandem Mass Spectrometry (ID-LC-MS/MS).
Dried urine spot strategy coupled with UHPLC-MS/MS for the analysis of troponin activators.
Network-based integration of metabolomics data from large-scale repositories.
KMD-Enhanced MALDI-ToF MS for Polymer Biodegradation Analysis.
Discovery and quantification of novel diazepam metabolites BP-246 and BP-271 in freshwater fish using HRMS and UPLC-MS/MS.
A high-throughput lC-MS/mS method for simultaneous determination of lumateperone and its four metabolites in human plasma: application to a clinical trial.
Development and Validation of a Sensitive UHPLC-MS/MS Analytical Method for Fulzerasib in Rat Plasma and its Application to Pharmacokinetics Studies.
A novel targeted high-throughput workflow for serum chemical mixture profiling in population exposome-wide association studies.
Spatial metabolomics - a metabolic microscope for respiratory medicine.
A fast high-throughput logP estimation method for peptide molecules based on liquid chromatography-mass spectrometry method.
A nanogram-sensitive workflow for oligonucleotide mass spectrometry using ion-pair-free nanoflow HILIC and RNase benchmarking.
Efficient on-site detection of nitazenes in hair: Integrating MCX pipette-tip solid-phase extraction with miniaturized mass spectrometry.
Direct‑injection UHPLC-MS/MS multiresidue method for the determination of 97 pesticides in groundwater and surface water.

Fa Yi Xue Za Zhi. 2026 Apr 25. pii: 1004-5619(2026)02-0130-05. [Epub ahead of print]42(2): 130-134

[Detection of Chlormezanone in Blood Using HPLC-MS/MS Method].

Yue Liu, Weiwei Liang, Huanhui Zhu, Tianfu He, Yuanyuan Tian, Cong Peng, Songcai Wang.

   OBJECTIVES: To establish a high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method for detecting chlormezanone in blood samples.
METHODS: Acetonitrile was added to the samples to precipitate proteins. After vortex and ultrasonication, the mixture was centrifuged, and the supernatant was collected. It was then filtered using a 0.22 μm polytetrafluoroethylene membrane. Separation was performed using an InfinityLab Poroshell 120 EC-C18 column (100 mm×4.6 mm, 2.7 μm). The mobile phase consisted of phase A (0.1% formic acid) and phase B (acetonitrile), with gradient elution at a flow rate of 0.4 mL/min. The mass spectrometer was operated with an electrospray ionization in positive ion mode and multiple reaction monitoring mode.
RESULTS: Chlormezanone in blood samples showed good linearity within the tested range, with the correlation coefficients (r) all greater than 0.999. The limit of detection and the limit of quantitation of chlormezanone were 22.83 ng/mL and 100 ng/mL, respectively. The matrix effects were 2.1%-3.9% and recoveries were 88.8%-92.3%. Using this method, the mass concentration mass of chlormezanone detected in a positive sample was 1 217.23 ng/mL.
CONCLUSIONS: This method requires simple sample preparation and a small sample volume, and offers a wide linear range, making it suitable for the detection of chlormezanone in blood.

Keywords:  blood; chlormezanone; forensic medicine; high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS); toxicological analysis

DOI:  https://doi.org/10.12116/j.issn.1004-5619.2024.340403
J Mass Spectrom. 2026 Aug;61(8): e70083

Development and Optimization of an LC-MS/MS Method for Quantification of Phosphatidylethanol in Human Whole Blood.

Jacob B Nielsen, Sarrah Lahorewala, Qingwen Yang, Hai Huynh, Yuvanesh Vedaraju, Yiwei Liu, Roger L Bertholf, Xin Yi.

  Phosphatidylethanols (PEth) are ethanol-derived phospholipids formed in red blood cell membranes during alcohol exposure and have emerged as highly specific biomarkers for recent alcohol use. Their extended 2-4-week detection window makes them uniquely valuable for objective monitoring in liver disease and transplantation, where accurate assessment of alcohol abstinence is critical. We developed and validated a robust liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay for simultaneous quantification of PEth 16:0/18:1 and PEth 16:0/18:2 in whole blood. Multiple sample extraction strategies were evaluated to optimize recovery, sensitivity, and workflow practicality. The final method employed phospholipid-removal cartridges in a reversed-use configuration to retain, rather than remove, phospholipids. Wash and elution conditions were systematically optimized to achieve adequate sensitivity without a post-extraction evaporation step, enabling direct LC-MS/MS loading after elution and automation compatibility. Due to detectable and lot-variable endogenous PEth in commercial human blood products, multiple matrix sources were evaluated. Chicken whole blood demonstrated the cleanest background and was selected for calibrator and quality-control preparation. The developed method achieved linearity from 10 to 1000 ng/mL (R2 > 0.99) with limits of quantification below 10 ng/mL, and within- and between-run precision of < 10% and < 12%, respectively. Method comparison against a national reference laboratory showed excellent agreement (R2 ≥ 0.93; bias within ± 5%). No significant carryover, ion suppression, or lipid interference was observed. This developed and optimized LC-MS/MS method provides a sensitive, simplified, and automation-compatible approach for PEth 16:0/18:1 and 16:0/18:2 quantification, well-suited for high-throughput implementation in clinical laboratories.

Keywords:  LC–MS/MS; alcohol biomarker; liver transplantation; phosphatidylethanol

DOI:  https://doi.org/10.1002/jms.70083
Anal Bioanal Chem. 2026 Jul 17.

Development and validation of a multi-matrix LC-MS/MS method for quantification of 20 drugs in human postmortem and porcine surrogate matrices.

Jeroen Roosendaal, Shirley Verschoor, Daan J Touw, Dick-Paul Kloos, Rogier van der Hulst.

  Alternative matrices are increasingly used in postmortem toxicology when conventional specimens such as femoral blood are unavailable. However, quantitative multi-matrix methods covering a wide range of tissues remain limited. This study describes the development and fit-for-purpose validation of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantification of 20 forensically relevant drugs in human and porcine postmortem matrices. Analytes and internal standards were extracted by methanol-based protein precipitation, followed by reversed-phase chromatography gradient separation and quantitation using a linear ion trap consisting of a quadrupole mass filter. A solvent calibration curve was used to analyze all matrices in a single analytical run. Validation was performed according to a modified fit-for-purpose approach focusing on accuracy, precision, selectivity, carry-over, matrix effect, dilution feasibility, and stability. Acceptance criteria were fulfilled for 89.3% of analyte-matrix combinations under standard criteria and 96.7% after predefined fit-for-purpose adjustments. Porcine matrices showed analytical performance comparable to human tissues, supporting their use as surrogate matrices for method development and validation. The developed LC-MS/MS method enables quantification of drugs across a broad range of alternative postmortem matrices using a single extraction and calibration approach. The method is intended for fast, reliable, and resource-efficient multi-matrix studies rather than absolute quantification in individual matrices and provides a practical tool for the investigation of postmortem redistribution processes.

Keywords:  Alternative matrices; Forensic toxicology; LC–MS/MS; Postmortem

DOI:  https://doi.org/10.1007/s00216-026-06664-2
Anal Chem. 2026 Jul 16.

Authentic Spatial Metabolomics by Avoiding Hidden Pitfalls in MSI Workflows.

Jinyu Zhou, Shengxi Li, Yinghao Cao, Qi Liu, Congmin Xu, Lin Wang.

Mass spectrometry imaging (MSI) has emerged as a powerful analytical tool for visualizing the spatial distribution of endogenous molecules in complex biological tissues. However, achieving authentic and reproducible metabolic maps remains challenging due to pitfalls in sample preparation and instrumental limitations that are often overlooked. Herein, based on practical evaluation, we delineate four critical but frequently overlooked pitfalls in MSI workflows: metabolic quenching, matrix effects, mass resolving power, and quadrupole isolation width. We demonstrate that thaw-mounting during traditional tissue preparation reactivates metabolic enzymes, which can be mitigated by rapid heat stabilization above 100 °C. Region-specific matrix effects causing uneven ionization could be corrected by normalization against isotope-labeled internal standards. Using incremental resolving power, we reveal that a single nominal m/z can represent multiple isobaric species with distinct spatial patterns, underscoring the necessity of ultrahigh resolution. Furthermore, we introduce a spatial correlation analysis that deconvolutes chimeric MS/MS spectra from coisolated precursors, enabling correct assignment of isobaric metabolites (e.g., choline and aminobutyric acid). Collectively, this study identifies four pitfalls and provides actionable strategies to overcome them, offering a practical framework for more reliable spatial metabolomics in preclinical and clinical research.

DOI: https://doi.org/10.1021/acs.analchem.6c03023
Bioinformatics. 2026 Jul 15. pii: btag520. [Epub ahead of print]

aiSysMet: AI-Powered Systems Metabolomics for Biomarker Discovery.

Habtom Ressom, Linge Yan, Hongyu Ao, Xinran Zhang, Sara Hashemi, Rency Varghese, Bardia Nezami, Dawit Mengistu.

MOTIVATION: Metabolomics plays an essential role in the growing systems biology approaches to unravel the relationships between metabolites and diseases. Liquid chromatography-mass spectrometry (LC-MS) is central to this effort because it can profile many metabolites from limited material. Yet, in a typical untargeted LC-MS-based metabolomics study, the majority of detected peaks remain unannotated, largely due to incomplete spectral libraries and uncertainties in peak picking, alignment, and the handling of isotopes and adducts. These limitations hinder seamless integration with other omics layers.
RESULTS: We developed an AI-powered platform (aiSysMet) that uses statistical, machine learning, and deep learning methods for metabolomics data processing, metabolite annotation, and integrative analysis of multi-omics data. The platform's interactive and modular web interface allows users to easily build data analysis pipelines that can be executed in the cloud.
AVAILABILITY: aiSysMet is freely available for non-commercial users on https://tools.omicscraft.com/aiSysMet.

DOI: https://doi.org/10.1093/bioinformatics/btag520
Adv Exp Med Biol. 2026 ;1501 525-554

Mass Spectrometry as a Tool for Metabolomics in Cancer.

João S Patrício, Ana C L Guerreiro, Paulo A Gameiro, Judit Morello.

  Mass spectrometry (MS) is a highly sensitive and high-throughput analytical technology that has become central to investigating the metabolic alterations in cancer cells, enabling the discovery of diagnostic biomarkers and potential therapeutic targets. This chapter provides an overview of the key principles of MS-based metabolomics, covering the entire experimental workflow-from sample collection and preparation to data acquisition, preprocessing, normalization, statistical modeling, and pathway enrichment analysis. We also discuss current limitations and outline future directions to enhance data reproducibility, metabolite annotation, and clinical translation of MS-based results.

Keywords:  Biomarkers; Cancer diagnosis; MS-based metabolomics; Mass spectrometry (MS)

DOI:  https://doi.org/10.1007/978-3-032-12166-0_19
Anal Bioanal Chem. 2026 Jul 14.

Improving detection of low-abundant pharmaceuticals and neurotransmitters via quadrupole isolation in MALDI mass spectrometry imaging.

Karina A Vargas, Sarah Diez, Michael Becker, Elizabeth K Neumann.

  Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a powerful tool for mapping the spatial distribution of pharmaceuticals and metabolites in tissue. However, its effectiveness in the low-mass range (< 400 m/z) is impacted by matrix interference and ion suppression, reducing signal-to-noise (S/N) ratios. To address this challenge, we assessed a targeted quadrupole isolation strategy using a MALDI q-TOF mass spectrometer. This approach selectively isolates narrow windows around individual analytes m/z to reduce background noise and enhance S/N, therefore generating a smaller selective ion packet to the TOF analyzer. We applied this method to detect acetaminophen, paracetamol sulfate, caffeine, paraxanthine, as well as dopamine and its metabolites (HVA, 3-MT, and DOPAC) within murine liver and brain tissue sections, respectively. We utilized a range of isolation windows (e.g., 1, 5, 10, 20, 100 m/z) around each target m/z value. This dynamic isolation significantly decreased chemical background without fragmenting the target ions. As a result, we achieved precise spatial localization of parent drugs and their metabolites. Compared to untargeted acquisition, this method improved S/N by over 50% for all analytes within ≤10 m/z isolation ranges, while preserving tissue morphology. This targeted isolation approach extends the capabilities of MALDI MSI and offers a robust and scalable solution for analyzing low-mass xenobiotics and metabolites in situ.

Keywords:  MALDI mass spectrometry imaging; MS/MS; Neurotransmitters; Quadrupole isolation; Small molecules

DOI:  https://doi.org/10.1007/s00216-026-06659-z
Anal Methods. 2026 Jul 17.

Quantification of catecholamines in human plasma using isotope dilution mass spectrometry with para-aminobenzoic acid-modified magnetic polydopa particles.

Jixing Huang, Xiaojie Zhang, Yazhou Han, Wentao He, Chunbo Liu, Chuan-Fan Ding, Yinghua Yan.

Measurement of low concentrations of catecholamines in biological samples remains a challenging task. In this study, a method combining magnetic solid-phase extraction (MSPE) with liquid chromatography tandem mass spectrometry (LC-MS/MS) was developed for the stable, convenient, and effective determination of catecholamines and their derivatives in human plasma. Dopamine (DA)- and para-aminobenzoic acid (PABA)-modified magnetic nanoparticles (Fe3O4@PDA@PABA) were prepared as adsorbents. The established method was subjected to comprehensive methodological validation using isotope dilution mass spectrometry. The limits of detection (LOD) and lower limits of quantification (LLOQ) were in the ranges of 0.01-0.05 ng mL-1 and 0.02-0.08 ng mL-1, respectively. Good linearity was achieved in the ranges of 0.05-10.00 ng mL-1 and 0.10-20.00 ng mL-1, with correlation coefficients (R2) ranging from 0.9952 to 0.9984. The extraction recoveries in plasma were between 85.55% and 105.00%. Consequently, a hybrid method integrating MSPE and LC-MS/MS was successfully established and applied for the quantitative analysis of catecholamines and their metabolites in human plasma.

DOI: https://doi.org/10.1039/d6ay00435k
Biomed Chromatogr. 2026 Sep;40(9): e70550

Validation of an UHPLC-MS/MS Assay for the Quantification of Isoniazid and Four Major Metabolites in Human Plasma.

David Nerguizian, Brandon Klein, Farah Abdelmawla, Joe Gomez, Peter L Anderson, Lane Bushman, Kristina M Brooks.

  Isoniazid (INH) is a key component of tuberculosis treatment regimens but is also associated with hepatotoxicity. This toxicity is mediated in part by its metabolites, but some degrade rapidly in plasma. A rapid freeze/thaw process with a methanol protein precipitation extraction was developed to slow the rapid degradation of acetylisoniazid (AcINH) into isonicotinic acid (INA) and acetylhydrazine (AcHZ) in human plasma. An assay consisting of two UHPLC-MS/MS methods was developed and validated to determine concentrations of INH and four of its metabolites in human plasma: the "polar" method covering AcINH and INA, and the "nonpolar" method covering p-tolualdehyde derivatized AcHZ, hydrazine (HZ), and INH. Polar and nonpolar method chromatographic separation was accomplished with biphenyl or C18 columns, respectively, mobile phases of 4 mM ammonium formate in water or acetonitrile, and method specific gradient conditions. The validated range for AcINH, INA, and INH was 10.0 to 5000 ng/mL and for AcHZ and HZ was 10.0 to 500 ng/mL from 0.1 mL of plasma, respectively. Though other groups have validated methods to quantitate some or all of these analytes, none have adequately characterized or addressed AcINH degradation. This validated assay will help facilitate a better understanding of INH metabolite disposition and relationships with toxicity.

Keywords:  UHPLC–MS/MS; acetylhydrazine; acetylisoniazid; hydrazine; isonicotinic acid

DOI:  https://doi.org/10.1002/bmc.70550
Molecules. 2026 Jun 29. pii: 2275. [Epub ahead of print]31(13):

Structure-Based Comparative Metabolomics Identifies LysoPE 15:0 as a Candidate Metabolite Marker of Influenza Virus Infection Dynamics.

Junxiao Wang, Yuting Li, Bin Wang, Wenxia Fang, Yushen Du, Fei Xu.

  Influenza virus outbreaks remain a persistent public health concern, yet traditional metabolomics methods are inadequate for addressing key analytical challenges of "dark matter" in influenza research. By integrating quantitative MS1 data, MS2-derived fragmentation trees and molecular fingerprints, structure-based comparative metabolomics enhances predictive capability for chemical structures, and enables the discovery of candidate metabolic markers without the need for database spectra. In this study, we established a C57BL/6J mouse model of H1N1 infection (with PBS as control) and performed structure-based comparative metabolomics on fecal samples using liquid chromatography-mass spectrometry (LC-MS). Quantitative analysis of MS1 data identified 40 differential metabolites, while qualitative analysis of MS2 data enabled their structural annotation. A candidate metabolite marker, LysoPE 15:0, along with other potential metabolic markers, was annotated and validated using Mirror plot, CFM-ID, and sim-Rank-Network. Our findings demonstrate that structure-based comparative metabolomics enables library spectra-free annotation of metabolomic "dark matter" and provides a methodological workflow for discovering candidate metabolite markers in other diseases.

Keywords:  candidate metabolite marker discovery; influenza virus; structure-based comparative metabolomics

DOI:  https://doi.org/10.3390/molecules31132275
J Mass Spectrom. 2026 Aug;61(8): e70088

A Metrologically Traceable Candidate Reference Measurement Procedure (cRMP) for Dehydroepiandrosterone Sulfate in Human Serum Based on Isotope Dilution-Liquid Chromatography-Tandem Mass Spectrometry (ID-LC-MS/MS).

Liping Yang, Bingling Gao, Tao Yang, Liping Tang, Ying Kan, Keqi Sun, Peng Xiao.

  Dehydroepiandrosterone sulfate (DHEAS), a crucial steroid hormone for adrenal function and pubertal development, is highly associated with related diseases. This study aims to develop and validate an isotope dilution liquid chromatography tandem mass spectrometry (ID-LC-MS/MS)-based candidate reference measurement procedure (cRMP) for quantifying serum DHEAS. Serum samples were prepared by protein precipitation with acetonitrile and separated on a reversed phase column. Assay validation was conducted under the guidance of standard documents, including C62-A, EP6-A, EP10-A3, and C50-P endorsed by the Clinical and Laboratory Standards Institute (CLSI). The cRMP was established and proven to be highly specific without significant matrix effect and able to accurately quantify DHEAS in human serum. The intra-assay and inter-assay imprecision ranged from < 0.1 to 1.0% and from 1.0 to 1.1%, respectively. Trueness was assessed by recovery rate from 99.6 to 101.2%. The limit of detection (LoD) was 0.270 nmol/L, and the lower limit of the measuring interval (LLMI) was 12.1 nmol/L. A linear correlation ranged from 7.60 to 41 858 nmol/L was observed with a correlation coefficient > 0.999. R2 value of linear regression analysis between this method and clinical immunoassays was ≥ 0.990. The relative expanded uncertainty was 1.5%-2.5% over the concentration range of 12.1-33 043 nmol/L. This study developed an ID-LC-MS/MS-based cRMP, which provided high specificity, trueness, and precision for serum DHEAS quantification, contributing to the DHEAS measurement standardization and traceability.

Keywords:  dehydroepiandrosterone sulfate; isotope dilution‐liquid chromatography–tandem mass spectrometry; reference measurement procedure; traceability

DOI:  https://doi.org/10.1002/jms.70088
J Chromatogr A. 2026 Jul 10. pii: S0021-9673(26)00591-1. [Epub ahead of print]1785 467262

Dried urine spot strategy coupled with UHPLC-MS/MS for the analysis of troponin activators.

Xiaoyun Zhang, Ning Xu, Mingxue Yang, Yunda Li, Xiaochen Huang, Yan Qiao, Guojun Li, Kaoqi Lian.

  A rapid, sensitive, and reliable analytical approach based on dried urine spot (DUS) sampling coupled with ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was established and fully validated for the simultaneous quantification of six troponin activators in human urine, following the WADA and FDA analytical guidelines. Key experimental parameters, including filter paper type, punch diameter, extraction solvent, solvent volume, and ultrasonic extraction time, were systematically optimized. Under the optimized conditions, all target analytes exhibited favorable linearity (R² > 0.99) in their respective ranges, and the limits of detection (LODs) were below 1 ng/mL for most compounds. The extraction recoveries of the six troponin activators ranged from 80.16% to 90.34%, and matrix effects were determined to be within the range of 82.76%-111.34%. Both intra-day and inter-day precision values were below 15%. Stability verification revealed that DUS samples possessed distinctly superior long-term stability compared with liquid urine samples under diverse storage conditions. The established DUS-UHPLC-MS/MS method features simple operation, minimal sample consumption, low solvent dosage, and excellent stability, making it well-suited for rapid screening and quantitative confirmation of troponin activator misuse in routine sports anti-doping analysis.

Keywords:  Anti-doping analysis; Dried urine spots; Method validation; Troponin activators; UHPLC-MS

DOI:  https://doi.org/10.1016/j.chroma.2026.467262
Metabolomics. 2026 Jul 15. pii: 127. [Epub ahead of print]22(4):

Network-based integration of metabolomics data from large-scale repositories.

Cecilia Wieder, Eloisa Rocha Liedl, Thomas Payne, Ozgur Yurekten, Callum Martin, Felix Xavier Amaladoss, Noemi Tejera, Wanchang Lin, Yasin El Abiead, Pieter Dorrestein, Claire O'Donovan, Juan Antonio Vizcaíno, Warwick Dunn, Timothy Ebbels.

   INTRODUCTION: Public metabolomics data repositories such as MetaboLights and Metabolomics Workbench host rapidly growing volumes of raw data, processed results, and metadata. As data deposition becomes a prerequisite for funding and publication, there is an increasing need for tools that enable integration and joint reanalysis of datasets across studies to maximise reuse and reproducibility.
OBJECTIVES: This study aims to enable large-scale integrative meta-analysis of public metabolomics data, exploiting harmonised metabolite annotations to identify robust multi-study metabolite and pathway signatures and to provide global visual overviews of repository content.
METHODS: We developed a network-based integration framework operating at both the study (dataset) level and the metabolite or pathway level. Metabolite-level meta-networks integrate studies with shared biological context using co-occurrences of differential metabolites represented as bipartite graphs. Study-level networks compare observed metabolites for overall repository exploration. Networks can be explored interactively using a dedicated Python Dash app available at https://github.com/EloisaRL/Metabolomic-data-analysis-app/tree/main .
RESULTS: As an example, the approach was applied to six COVID-19 plasma datasets from MetaboLights generated using LC-MS and NMR. Ten metabolites were identified as differential in at least three studies, including consistently up-regulated pyroglutamic acid, in agreement with the literature. Pathway-level networks provided an overview of shared biological processes across studies. A global network of 1,181 studies in Metabolomics Workbench demonstrated clustering by assay coverage and associated metadata, as expected.
CONCLUSION: Network-based integration of harmonised metabolomics data enables robust cross-study analyses and highlights the critical importance of standardised annotation pipelines. Such approaches enhance the reuse, reproducibility, and impact of public metabolomics datasets, accelerating biological discovery.

Keywords:  Data integration; Harmonised annotation; Networks; Public data reuse; Repositories

DOI:  https://doi.org/10.1007/s11306-026-02507-4
J Am Soc Mass Spectrom. 2026 Jul 14.

KMD-Enhanced MALDI-ToF MS for Polymer Biodegradation Analysis.

Sophia Y van Mourik, Heather J Walker, Anthony J Ryan.

  A novel and tailored mass spectrometry workflow is presented for the analysis of polymer biodegradation products, integrating principles from the 'omics' sciences to address the challenges of complex mixture characterization. The workflow combines methodologies from polymer analysis and metabolomics, offering a comprehensive approach to data acquisition and processing, with practical considerations for user implementation. Central to the analytical strategy is the application of Kendrick Mass Defect (KMD) theory, which enhances spectral visualization and facilitates the identification of biodegradation products and metabolites within heterogeneous samples. By combining accessible and open software tools along with custom R scripts, the workflow supports reproducible MS data analysis, providing a platform for advancing polymer biodegradation research. Biodegraded samples, due to their complex polymer and metabolite content, typically generate noisy spectra, which require intensive filtering to distinguish polymer fragments from microbial metabolites. While pure polymer spectra are generally cleaner, they still necessitate specific peak detection methods, emphasizing the need for tailored data processing protocols.

Keywords:  Biodegradation; Kendrick Mass Defect Analysis; MALDI-ToF MS; Oligomer Characterization; Polymer Degradation Mechanisms

DOI:  https://doi.org/10.1021/jasms.6c00101
Sci Rep. 2026 Jul 13.

Discovery and quantification of novel diazepam metabolites BP-246 and BP-271 in freshwater fish using HRMS and UPLC-MS/MS.

Ping Ouyang, Junlin Wang, Nianhua Zhang, Zhengyan Hu, Changren Ye, Dingnan Wang, Yang Wang, Pinggu Wu.

  Diazepam, commonly used in freshwater fish transport and aquaculture, poses potential food safety and public health risks due to its residues and metabolites. However, current monitoring efforts primarily focus on the parent drug and its major metabolites, leaving potential toxic transformation products uncharacterized. This study reports two novel metabolites (BP-246, 5-chloro-2-(methylamino)phenyl)(phenyl)methanone, and BP-271, 6-chloro-1-methyl-4-phenylquinazolin-2(1 H)-one) in freshwater fish muscle, a matrix in which these compounds have not been previously reported, using liquid chromatography-Orbitrap high-resolution mass spectrometry (LC-Orbitrap HRMS). Using ProTox3.0 and ADMETlab3.0 for toxicity prediction revealed that BP-246 and BP-271 exhibit high blood-brain barrier permeability, neurotoxicity and ecotoxicity. A sensitive and validated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed for the simultaneous quantification of diazepam, three established metabolites (nordiazepam, oxazepam, temazepam), and the two novel compounds in fish tissue. Sample preparation involved acetonitrile ultrasonication extraction followed by solid-phase extraction (SPE) purification. Matrix-matched calibration curves demonstrated excellent linearity ( R2 > 0.999) over the range of 0.2-10 µg/kg. Method recovery ranged from 78.5% to 119.9%, with intra-day and inter-day relative standard deviations (RSDs) below 9.9% and 9.1%, respectively. Limits of detection (LOD) and quantification (LOQ) were 0.05-0.06 µg/kg and 0.15-0.20 µg/kg, respectively. The method showed robust selectivity and consistent retention times. When applied to 10 market-sourced, diazepam-positive fish samples, the method successfully revealed differential metabolite profiles, enabling rapid, high-throughput monitoring of diazepam and transformation products in commercial fish products. These findings provide a basis for comprehensive risk assessment and regulatory control of diazepam residues in the food supply chain.

Keywords:  Diazepam; Fish; HRMS; Novel metabolite; UPLC-MS/MS

DOI:  https://doi.org/10.1038/s41598-026-61635-y
Xenobiotica. 2026 Jul 15. 1-18

A high-throughput lC-MS/mS method for simultaneous determination of lumateperone and its four metabolites in human plasma: application to a clinical trial.

Hongjie Ding, Bingda Wu, Rui Wang, Chenxin Ding, Pengfei Zhang, Juefang Ding, Li Ding, Yunli Zhao.

  1. Lumateperone is an antipsychotic metabolised to four active metabolites IC200131, IC200161, IC200565 and IC201308, which are closely related to its clinical efficacy and safety.2. For evaluating the clinical pharmacokinetics of lumateperone and its active metabolites in Chinese subjects, a high-throughput LC-MS/MS method was developed and validated for the simultaneous quantification of lumateperone and its four metabolites in human plasma. Chromatographic separation was achieved using an alkaline mobile phase and a bidentate silane column (Zorbax Extend-C18) with two-step gradient elution, which overcame peak tailing and carryover while enabling rapid analysis. The calibration ranges were 0.100-80.0 ng/mL for lumateperone and IC200131, 0.0400-32.0 ng/mL for IC200161 and IC201308, and 0.150-30.0 ng/mL for IC200565.3. The validated method was successfully applied to a pharmacokinetic study of lumateperone tosylate capsules. The clinical trial was registered at the Chinese Clinical Trial Registry (identifier: CTR20242699). Under fasting conditions, the mean Cmax values were 30.6 ng/mL for lumateperone, with corresponding AUC0-t values of 72.8 h·ng/mL. Under fed conditions, food delayed absorption and decreased Cmax for all analytes.4. This study reports the first comprehensive pharmacokinetic profiles of lumateperone and its four active metabolites in Chinese subjects. The validated method provides a robust foundation for pharmacokinetic research of lumateperone in humans.

Keywords:  IC200131; IC200161; IC200565; IC201308; LC-MS/ms; Lumateperone; metabolites; pharmacokinetics

DOI:  https://doi.org/10.1080/00498254.2026.2704032
Biomed Chromatogr. 2026 Aug;40(8): e70552

Development and Validation of a Sensitive UHPLC-MS/MS Analytical Method for Fulzerasib in Rat Plasma and its Application to Pharmacokinetics Studies.

Qiang Liu, Jin-Zhu Zhao, Li Wang, Fu-Sheng Zhou, Jiong Lan, Qiang Lu, Tao Jiang, Hong-Can Ren.

  Fulzerasib is a novel, potent, and irreversible covalent inhibitor targeting the KRAS G12C mutation, recently approved in China for advanced nonsmall cell lung cancer. This study aimed to develop and fully validate a rapid, specific and sensitive UHPLC-MS/MS method for the quantification of Fulzerasib in rat plasma. Sample preparation was streamlined using a simple protein precipitation technique with acetonitrile. Chromatographic separation was achieved within a 4.0-min run on a C18 column, with verapamil as the internal standard and detection via multiple reaction monitoring. The method was rigorously validated over a linear range of 5 to 5000 ng/mL (R2 > 0.9933), demonstrating excellent accuracy (102%-112.7%) and precision (≤ 10.3% for QCs). Stability was confirmed under various storage and processing conditions. The validated method was successfully applied in the first pharmacokinetic study of Fulzerasib in Sprague-Dawley rats following single intravenous (1 mg/kg) and oral (3 mg/kg) administration. Fulzerasib exhibited favorable pharmacokinetic properties, including low plasma clearance (5.02 mL/min/kg), moderate volume of distribution and notably high oral bioavailability of 38.6%. The established method is reliable, efficient and readily applicable, thereby providing a vital tool for accelerating the ongoing preclinical and translational research of Fulzerasib.

Keywords:  KRAS G12C inhibitor; UHPLC‐MS/MS; pharmacokinetics

DOI:  https://doi.org/10.1002/bmc.70552
Talanta. 2026 Jul 08. pii: S0039-9140(26)00931-8. [Epub ahead of print]311 130275

A novel targeted high-throughput workflow for serum chemical mixture profiling in population exposome-wide association studies.

Yan Wu, Linlin Chen, Jie Zhang, Lisong Chen, Shanshan Du, Rui Ding, Weimin Ye.

  Simultaneous determination of environmental pollutants with complex compositions and wide-ranging acid dissociation constants in biological matrices presents a significant analytical challenge. This study developed a highly sensitive and broad-spectrum analytical method based on ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). By employing phospholipid removal purification (PRP) technology and optimizing mobile phase pH conditions, we achieved simultaneous quantification of 230 environmental pollutants in serum. Comparative evaluation of sample pretreatment techniques revealed that low-temperature concentration caused preservative loss, while liquid-liquid extraction showed poor recovery for multiple compound classes. The PRP method was selected as the optimal approach due to its superior performance in reducing matrix effects compared to direct protein precipitation. Method validation demonstrated accurate quantification of all target analytes (relative standard deviation, RSD <15.1%), with 98.3% of compounds exhibiting satisfactory recoveries (80-120%). Analysis of serum samples from the Fuqing cohort participants detected 22 contaminants with detection frequencies >30%, among which PFHpA and PFOA were identified as risk factors for hyperuricemia. Notably, we provide the first evidence of a dose-response relationship between dehydroacetic acid exposure and hyperuricemia prevalence in a human population. This study established a robust solution for simultaneous screening of exposome-scale pollutants in complex biological samples.

Keywords:  Dehydroacetic acid; Exposome-wide; Hyperuricemia; Multi-pollutant; Target exposome

DOI:  https://doi.org/10.1016/j.talanta.2026.130275
Am J Respir Cell Mol Biol. 2026 Jul 11. pii: aanag143. [Epub ahead of print]

Spatial metabolomics - a metabolic microscope for respiratory medicine.

Matthew J Smith, Jesper Säfholm, Craig E Wheelock.

Spatial metabolomics enables in situ, pixel-resolved mapping of small molecules across tissues, providing a powerful complement to conventional bulk metabolomics, which lacks cellular and anatomical resolution. By adapting mass spectrometry (MS) ionization approaches such as matrix-assisted laser desorption/ionization (MALDI) and desorption electrospray ionization (DESI), spatial metabolomics generates high-resolution metabolic maps that link metabolite distributions to defined tissue regions, cellular niches, and biological functions. This "metabolic microscopy" enables localization of biosynthetic pathways, identification of region-specific metabolic signatures, and integration with histology and other spatial omics modalities. High-resolution MS platforms support untargeted discovery, while targeted approaches enable sensitive detection of low-abundance metabolites. In respiratory research, spatial metabolomics has begun to reveal regional heterogeneity in lung metabolism, including surfactant remodeling, lipid mediator localization, fibrosis-associated metabolic reprogramming, infection-specific airway responses, and tumor-associated phospholipid dysregulation. These studies highlight the capacity of the method to connect localized biochemistry with pulmonary physiology and disease mechanisms. However, challenges remain, including limited sensitivity, difficulties in metabolite identification and isomer discrimination, restricted quantification strategies, and incompatibility with commonly used FFPE tissue preservation, underscoring the need for standardized fresh-frozen tissue workflows. Future integration of spatial metabolomics with spatial transcriptomics and proteomics promises comprehensive, multi-layered metabolic mapping of the airways, enabling the cross talk between multiple orders of biology to be understood from specific tissue microenvironments. As part of a multimodal spatial biology framework, spatial metabolomics has strong potential to define disease endotypes, inform therapeutic target discovery, and generate spatial metabolic atlases that advance mechanistic understanding and precision medicine in respiratory disease.

DOI: https://doi.org/10.1093/ajrcmb/aanag143
Med Chem Res. 2026 Apr;35(4): 765-769

A fast high-throughput logP estimation method for peptide molecules based on liquid chromatography-mass spectrometry method.

Jing Deng, Hengmao Zhang, Yixuan Zhai, Wenbo Sun, Jin Li, Guansai Liu, Wei Tang.

  We have developed a complete end-to-end high-throughput protocol for rapid estimation of logP values of peptide molecules. This scheme combines two core technologies: firstly, the "pool and split" high-throughput synthesis technology is used to efficiently prepare peptide samples; secondly, a logP detection method based on ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS) was developed, which relies on high-resolution mass spectrometry to accurately identify hundreds of components in mixed samples. In addition, we innovatively established a linear correlation model between chromatographic capacity factor logK' and logP, which has an excellent correlation (R² = 0.92) and can accelerate fully automated data analysis. Finally, we successfully synthesized and detected mixed samples containing 16, 81, and 256 peptide molecules, with a logP detection rate exceeding 85%. The sample processing capacity of this detection system can exceed 20000 per day, which can significantly accelerate the early screening process of lead molecules in drug development.

Keywords:  High-throughput synthesis; LogP; Peptide; UPLC-MS

DOI:  https://doi.org/10.1007/s00044-026-03530-9
Nucleic Acids Res. 2026 Jul 03. pii: gkag691. [Epub ahead of print]54(13):

A nanogram-sensitive workflow for oligonucleotide mass spectrometry using ion-pair-free nanoflow HILIC and RNase benchmarking.

Yuyang Qi, Chengkang Li, Nur Yesiltac-Tosun, Jannick Schicktanz, Leona Rusling, Steffen Kaiser, Samuel Wein, Stefanie Kaiser.

RNA modifications regulate diverse cellular processes, yet comprehensive characterization of modified RNA sequences remains technically challenging. Mass spectrometry provides direct chemical information on RNA, but current oligonucleotide-based workflows typically require micrograms of RNA input and often rely on ion-pairing reagents for chromatographic separation, limiting their applicability to scarce or native RNA samples. Here, we establish a sensitive oligonucleotide mass spectrometry workflow that combines ion-pair-free nanoflow hydrophilic interaction liquid chromatography with systematic benchmarking of controlled RNA cleavage strategies. We compared RNase T1, RNase 4, and colicin E5 and evaluated how reaction conditions influence cleavage specificity, fragment length distribution, and terminal chemistries of RNA hydrolysates. The resulting workflow enables robust LC-MS/MS analysis using standard MS-compatible buffers and supports confident oligonucleotide identification through NucleicAcidSearchEngine (NASE) database searching. Using this approach, we achieved high sequence coverage from nanogram-scale RNA inputs, enabling modification analysis of 25-50 ng native yeast tRNAPhe and sequence verification of 250 ng synthetic mRNA. Together, this work establishes a sensitive and broadly applicable platform for oligonucleotide mass spectrometry and provides practical guidance for RNase selection and digestion strategies. The method expands the applicability of RNA MS to low-input samples and supports future studies of RNA sequence and modification landscapes.

DOI: https://doi.org/10.1093/nar/gkag691
Talanta. 2026 Jul 09. pii: S0039-9140(26)00940-9. [Epub ahead of print]311 130284

Efficient on-site detection of nitazenes in hair: Integrating MCX pipette-tip solid-phase extraction with miniaturized mass spectrometry.

Mengyao Tang, Yunfeng Zhang, Zhendong Hua, Wei Jia, Na Wang, Boyu Huang, Haixing Wang, Cuimei Liu.

  As a emerging class of synthetic opioids, nitazenes have witnessed an alarming global proliferation in the illicit drug market, posing severe threats to public health and social stability. Consequently, there is an urgent and growing demand for robust on-site rapid detection methods targeting these substances, especially within complex biological matrices. Herein, we report the first development of a miniaturized mass spectrometry (miniMS)-based analytical platform enabling rapid, on-site detection of 16 nitazenes in hair samples for the first time. Micropulverized extraction solvents and key MS parameters of the miniMS coupled with nano-electrospray ionization (nano-ESI) were systematically optimized. The limits of detection (LODs) and limits of quantification (LOQs) of miniMS for the 16 nitazenes in hair matrix ranged from 5 ng/mL to 20 ng/mL, and 20 to 80 ng/mL. Mixed-acidic cation-exchange pipette-tip solid-phase extraction (MCX PT-SPE) was successfully applied, yielding enrichment factors ranging from 6.7 to 9.9-fold across the various target analytes. Following integration with MCX PT-SPE, the miniMS method achieved a 94% true positive detection rate for 28 authentic hair samples (0.27 ng/mg to 8.56 ng/mg), represented a 38% increase compared to un-enrichment analysis. The linear ranges of individual analytes predominantly fell from their respective LOQs to 500 ng/mL, with the coefficient of determination (r2) exceeding 0.99. Precision ranged from 6.9% to 14.2% across all analytes. The Relative errors of quantitative results, calculated by comparing miniMS and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) for 8 authentic hair samples, ranged from -11.3% to 18.8%. The total analytical turnaround time for one single hair sample was within 10 min, with an additional 5 min required if the enrichment procedure was implemented. Compared with conventional techniques, this method enables on-site rapid detection while offering enhanced operational simplicity, high sensitivity, and portability, thereby demonstrating promising application prospects in drug crime investigation and forensic science.

Keywords:  MCX pipette-tip based solid-phase extraction; Miniaturized mass spectrometer; Nitazenes; On-site detection

DOI:  https://doi.org/10.1016/j.talanta.2026.130284
J Chromatogr A. 2026 Jul 10. pii: S0021-9673(26)00593-5. [Epub ahead of print]1785 467264

Direct‑injection UHPLC-MS/MS multiresidue method for the determination of 97 pesticides in groundwater and surface water.

Annamaria Ragonese, Claudia Campanale, Carmine Massarelli.

  A direct-injection UHPLC-MS/MS method was developed and validated for the simultaneous determination of 97 pesticides in groundwater and surface water. By bypassing time-consuming SPE and injecting samples directly, the proposed workflow achieves high-throughput performance without compromising regulatory sensitivity. Chromatographic separation was achieved within an 11 min active gradient, followed by a 6 min re-equilibration phase, resulting in a total cycle time of 17 min at 0.300 mL/min and 25 °C, while detection was performed on a triple-quadrupole mass spectrometer operating in SRM mode with rapid polarity switching. Calibration was carried out using matrix-matched calibration solutions applying a weighted (1/x) linear regression to compensate for heteroskedasticity and ensure accuracy at trace levels. The method achieved LOQs between 0.005 and 0.025 µg/L, fully meeting the requirement of LOQ ≤ 1/3 of the Italian EQS. Expanded uncertainties (k = 2) ranged from 18 to 19%, well below the 50% limit established by Legislative Decree 219/2010. Recoveries were between 87 and 98% with RSDs < 15% across all analytes and matrices. The workflow provides robust, sensitive, and regulation-compliant monitoring of pesticides in water bodies, enabling high-throughput analysis without any pre-concentration step.

Keywords:  Direct injection; Environmental monitoring; Groundwater; Matrix effects; Pesticides; Surface water; UHPLC–MS/MS

DOI:  https://doi.org/10.1016/j.chroma.2026.467264