bims-metlip 2025-09-14 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2025–09–14
nineteen papers selected by
Sofia Costa, Matterworks

Quantification of Trans- and Cis-Vitamin K1 Isomers in Human Plasma by a Rapid and Sensitive LC-MS/MS Method With Surrogate Matrix.
Development and Validation of an HPLC-MS/MS Method for Quantitative Bioanalysis of Lidocaine and its Metabolites in Human Plasma: Application in a Population Pharmacokinetic Study.
rtmsEcho: An Open-Source R Package for Automated Analysis of Acoustic Ejection Mass Spectrometry Data.
A Sensitive and Comprehensive LC-MS/MS Method for the Analysis of Hallucinogens, Synthetic Cathinones, and Synthetic Cannabinoids in Urine Samples.
Metabolomics in Endocrinology: The Way Forward.
An LC-MS/MS Assay of Irsenontrine, a Novel Phosphodiesterase‑9 Inhibitor, in Human Plasma, Urine and Cerebrospinal Fluid for Application to Clinical Pharmacokinetic Studies.
HT SpaceM: A high-throughput and reproducible method for small-molecule single-cell metabolomics.
Development and Validation of an LC-MS/MS Method for the Simultaneous Determination of Alprazolam, Bromazepam, Clonazepam, Diazepam and Flunitrazpam in Human Urine and Its Application to Samples from Suspected Drug Abusers.
Simultaneous determination of ten sweeteners in soybean products using PRiME HLB purification combined with ultra-high-performance liquid chromatography-tandem mass spectrometry.
Chemical Tagging with Mass Spectrometry Analysis for Sensitive Determination of Carboxylic Enantiomers in Hepatic Fibrosis.
Online solid-phase extraction coupled to liquid chromatography and tandem-mass spectrometry for the determination of glyphosate and other polar pesticide residues in plant commodities.
Elaboration of trapping conditions on zirconia for the online SPE-LC-MS/MS analysis of glyphosate and other polar organophosphonate and -phosphinate pesticide residues in plant-based food extracts.
Impact of injection solvent composition on 90 pesticides by LC-MS/MS: A data-driven framework for initial method development.
Analytical Techniques for Methyldopa and Metabolites: A Comprehensive Review.
A versatile toolkit for drug metabolism studies with GNPS2: from drug development to clinical monitoring.
De-MSI: A Deep Learning-Based Data Denoising Method to Enhance Mass Spectrometry Imaging by Leveraging the Chemical Prior Knowledge.
SLIM Ion Mobility-Based Analysis of Low Molecular Weight Explosives.
A New Approach to Large Multiomics Data Integration.
Metabolic Stability and Comprehensive Metabolite Profiling of Chrysotobibenzyl in Human Liver Microsomes and Hepatocytes Employing UPLC-MS/MS and UPLC-Orbitrap-HRMS Analysis.

Biomed Chromatogr. 2025 Oct;39(10): e70209

Quantification of Trans- and Cis-Vitamin K1 Isomers in Human Plasma by a Rapid and Sensitive LC-MS/MS Method With Surrogate Matrix.

Yi Jin, Zibin Song, Hanqi Du, Jing Zhuo, Xingyue Zhang, Yue Wang, Haiyan Xu, Xiumei Lu.

  A rapid and specific liquid chromatography-tandem mass spectrometry method with a wide linear range was developed and validated for the simultaneous quantification of Vitamin K1 (VK1) trans- and cis- isomers in human plasma. Bovine serum albumin solution (15%) served as a surrogate matrix for preparing the calibrators to establish the quantitative curves. After liquid-liquid extraction, VK1 trans- and cis- isomers in plasma samples were separated on a ChromCore C30 column (15 cm × 4.6 mm, 3 μm) using water: methanol: acetonitrile: formic acid (5:80:20:0.1, v/v/v/v) as the mobile phase. Mass spectrometry detection was performed in positive ion mode with atmospheric pressure chemical ionization (APCI) interface by multiple reaction monitoring (MRM) method. The calibration curves were linear over the range of 0.400-6000 ng/mL for the trans-isomer and 0.400-1200 ng/mL for the cis-isomer (r ≥ 0.994). The intra- and inter-day precision was below 9.55% in terms of relative standard deviation (RSD%) and the accuracy was within ±11.24% in terms of relative error (RE%). The selectivity, sensitivity, extraction recovery, matrix effect, dilution reliability, and stability met the acceptable criteria. The reliable LC-MS/MS method for concurrent detection of VK1 trans- and cis- isomers was successfully employed in a pharmacokinetic study in healthy Chinese volunteers after oral administration of 10 mg VK1.

Keywords:  LC–MS/MS; VK1; pharmacokinetics; surrogate matrix; trans‐ and cis‐ isomer

DOI:  https://doi.org/10.1002/bmc.70209
Eur J Drug Metab Pharmacokinet. 2025 Sep 12.

Development and Validation of an HPLC-MS/MS Method for Quantitative Bioanalysis of Lidocaine and its Metabolites in Human Plasma: Application in a Population Pharmacokinetic Study.

Keng Wah Foong, Didi Erwandi Mohamad Haron, Sook Hui Chaw, Yoke Lin Lo, Noridayu Omer, Pui San Loh.

BACKGROUND AND OBJECTIVE: Lidocaine is increasingly used perioperatively as a systemic analgesic. Quantification of lidocaine and its active metabolites, monoethylglycinexylidide (MEGX) and glycinexylidide (GX), is essential for understanding its pharmacokinetics and pharmacodynamics. Existing methods have limitations in throughput, concentration ranges, or do not simultaneously measure lidocaine and metabolites. This study aims to develop and validate a simple, rapid, and robust high-performance liquid chromatography-mass spectrometry (HPLC-MS)/MS method for their simultaneous quantification in plasma from surgical patients receiving intravenous lidocaine.
METHODS: Analytes were extracted from 75 µL of plasma by protein precipitation with 300 µL of methanol containing lidocaine-d10 (internal standard). After centrifugation for 5 minutes and filtration, 5 µL was injected onto a Phenomenex Luna C8(2) column (100 × 2.0 mm, 5 µm), achieving chromatographic separation within 5 minutes by gradient elution with 0.01% formic acid in water (mobile phase A) and acetonitrile-methanol 50:50 (mobile phase B). Mass spectrometry detection employed positive electrospray ionization with multiple reaction monitoring. The method uses a widely accessible HPLC-MS/MS platform, requires low plasma volume, and features streamlined sample preparation.
RESULTS: This method demonstrated good selectivity and specificity, minimal carryover, and reproducible recovery and matrix effects. Calibration curves were linear over 0.01-5 mg/L for lidocaine and 0.01-1.5 mg/L for MEGX and GX. Within-day and between-day accuracy and precision met acceptance criteria, and analytes remained stable under relevant conditions.
CONCLUSIONS: This validated assay requires low plasma volume and minimal preparation for simultaneous quantification of lidocaine and metabolites. It was successfully applied in a population pharmacokinetic study of surgical patients receiving intravenous lidocaine, supporting optimized dosing strategies.

DOI: https://doi.org/10.1007/s13318-025-00964-1
Anal Chem. 2025 Sep 12.

rtmsEcho: An Open-Source R Package for Automated Analysis of Acoustic Ejection Mass Spectrometry Data.

Mary Ashley Rimmer, Nathaniel Twarog, Tharindu A Ranathunge, Jingheng Wang, Yong Li, Taosheng Chen, Anang A Shelat, Lei Yang.

Mass spectrometry (MS) is a well-established technology in biological research, enabling the sensitive and precise quantitative analysis of complex samples. While traditional LC-MS systems provide robust performance for targeted analyses, their reliance on chromatographic separation limits throughput, rendering large-scale studies inefficient. The emergence of Acoustic Ejection Mass Spectrometry (AEMS) has revolutionized high-throughput workflows by eliminating chromatography and enabling direct nanoliter-scale sampling, achieving hundreds to thousands of measurements per hour. However, AEMS's full potential remains constrained by software limitations─existing tools lack robust automated processing capabilities for critical tasks such as peak detection, integration, and multimodal data analysis (e.g., multiple reaction monitoring, precursor ion, and neutral loss scans). To address this gap, we developed rtmsEcho, an open-source R package that extends our previously published rtms framework. This specialized solution provides direct access to AEMS data, enabling customizable processing of both MRM and full-scan acquisitions (precursor ion and neutral loss modes) while automating shot-to-peak association and spectral analysis. By streamlining data extraction and quantification, rtmsEcho enhances efficiency and reproducibility in high-throughput applications, including drug discovery, quality control, and clinical diagnostics. This innovation bridges a critical gap in AEMS data analysis, allowing researchers to fully leverage the speed and precision of next-generation mass spectrometry.

DOI: https://doi.org/10.1021/acs.analchem.5c03730
J Mass Spectrom. 2025 Oct;60(10): e5178

A Sensitive and Comprehensive LC-MS/MS Method for the Analysis of Hallucinogens, Synthetic Cathinones, and Synthetic Cannabinoids in Urine Samples.

Bruno Pereira Dos Santos, Letícia Birk, Vítor Camargo Pôrto, Sabrina Nunes Nascimento, Viviane Cristina Sebben, Sarah Eller, Tiago Franco de Oliveira.

  The laboratory analysis of new psychoactive substances and related drugs is crucial for accurate clinical and forensic diagnosis of poisonings. Given this, a new LC-MS/MS method for analyzing hallucinogens, synthetic cathinones, and synthetic cannabinoids in urine was developed. Urine samples were extracted using a liquid-liquid extraction protocol optimized via a multivariate experimental design. An aliquot of 400 μL of urine was enzymatically hydrolyzed with β-glucuronidase and extracted with 700 μL of ethyl acetate. The resulting extracts were analyzed using LC-MS/MS, with a total chromatographic run time of 8 min. The method was validated according to the ANSI/ASB Standard 036 guideline and was applied to 24 samples from suspected poisoning cases. The lower limits of quantification ranged from 0.1 to 1 ng/mL. Within-run and between-run precision (CV) were < 16%, and bias ranged from -12.8% to 19.8%. Nine of the 20 analytes investigated showed significant ionization suppression or enhancement (> 25%). Only two analytes (2C-E and 2-oxo-3-OH-LSD) had a recovery rate lower than 70%. Among the 24 analyzed urine samples, one tested positive for 25B-NBOH, one for LSD, and two for 2-oxo-3-OH-LSD. The developed method enables the simultaneous quantification of 20 illicit drugs, serving as an efficient diagnostic tool for clinical and forensic laboratories.

Keywords:  LC‐MS/MS; drug analysis; new psychoactive substances; urine

DOI:  https://doi.org/10.1002/jms.5178
Indian J Endocrinol Metab. 2025 Jul-Aug;29(4):29(4): 394-401

Metabolomics in Endocrinology: The Way Forward.

Shinjan Patra, Deep Dutta, Sanjay Kalra.

  Metabolomics is a type of laboratory science used to understand the cellular and metabolic defects in any disease process. It comprehensively identifies endogenous and exogenous low-molecular-weight (<1 kDa) molecules or metabolites in a high-throughput manner. Mass spectrometry-based methods are used for metabolomics which can be targeted and non-targeted. Metabolomics workflow consists of sample acquisition, its preparation and extraction, separation, ionisation, data analysis, and metabolite detection and identification. Some of the commonly elevated metabolomes are branched-chain amino acids like isoleucine, leucine, and valine in diabetes, carnitine and glutamate in osteoporosis, deoxycholic acid and betahydroxybutyrate in pituitary tumours, glutamic acid, valine, isoleucine for malignant thyroid nodules, L-asparagine, L-glutamine, dimethylarginine for hyperparathyroidism, tetrahydro-11-doxycortisol for adrenal tumours, and oxidised glutathione for hypogonadism. Knowing metabolomics can help us formulate personalised treatment choices for precision medicine in endocrinology. The main challenge ahead of metabolomics is its technical complexity and cost-benefit issues.

Keywords:  Diabetes; endocrinology; laboratory science; low-molecular-weight molecules; metabolomics; osteoporosis

DOI:  https://doi.org/10.4103/ijem.ijem_488_24
ACS Omega. 2025 Sep 02. 10(34): 39097-39104

An LC-MS/MS Assay of Irsenontrine, a Novel Phosphodiesterase‑9 Inhibitor, in Human Plasma, Urine and Cerebrospinal Fluid for Application to Clinical Pharmacokinetic Studies.

Koichiro Hotta, Karolina Doda, Jagadeesh Aluri, Yuji Mano.

Irsenontrine is a novel phosphodiesterase-9 inhibitor that has been developed for the treatment of cognitive dysfunction. To assess the pharmacokinetics, excretion, and distribution of the drug in humans, comprehensive assays for irsenontrine were developed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) in three human matrices, including plasma, urine, and cerebrospinal fluid (CSF). Irsenontrine was extracted from the matrices by a straightforward protein precipitation method and subsequently separated on a reverse-phase column. The analytes, irsenontrine and the deuterated stable isotope as the internal standard, were detected by LC-MS/MS in multiple reaction monitoring. The assay demonstrated the quantifiable detection of irsenontrine in plasma, urine, and CSF samples at concentrations as low as 2 ng/mL, with a run time of only 4 min. The assays exhibited satisfactory reproducibility, with accuracy and precision within the acceptable limits. The assays were employed for the purpose of determining the concentrations of irsenontrine in the three matrices, in support of clinical trials. Furthermore, the incurred sample reanalysis further demonstrated the reproducibility of the assays.

DOI: https://doi.org/10.1021/acsomega.5c05431
Cell. 2025 Sep 02. pii: S0092-8674(25)00929-8. [Epub ahead of print]

HT SpaceM: A high-throughput and reproducible method for small-molecule single-cell metabolomics.

Jeany Delafiori, Mohammed Shahraz, Andreas Eisenbarth, Volker Hilsenstein, Bernhard Drotleff, Alberto Bailoni, Bishoy Wadie, Måns Ekelöf, Alexander Mattausch, Theodore Alexandrov.

  Single-cell metabolomics (SCM) promises to reveal metabolism in its complexity and heterogeneity, yet current methods struggle with detecting small-molecule metabolites, throughput, and reproducibility. Addressing these gaps, we developed HT SpaceM, a high-throughput SCM method combining cell preparation on custom glass slides, small-molecule matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (MS), and batch processing. We propose a unified framework covering quality control, characterization, structural validation, and differential and functional analyses. Profiling HeLa and NIH3T3 cells, we detected 73 small-molecule metabolites validated by bulk liquid chromatography tandem MS (LC-MS/MS), achieving high reproducibility and single-cell resolution. Interrogating nine NCI-60 cancer cell lines and HeLa, we identified cell-type markers in subpopulations and metabolic hubs. Upon inhibiting glycolysis in HeLa cells, we observed emerging glucose-centered metabolic coordination and intra-condition heterogeneity. Overall, we demonstrate how HT SpaceM enables robust, large-scale SCM across over 140,000 cells from 132 samples and provide guidance on how to interpret metabolic insights beyond population averages.

Keywords:  LC-MS/MS; MALDI-imaging mass spectrometry; NCI-60; SpaceM; co-abundance; heterogeneity; high-throughput; reproducibility; single-cell metabolomics; small-molecule metabolites

DOI:  https://doi.org/10.1016/j.cell.2025.08.015
Molecules. 2025 Aug 22. pii: 3451. [Epub ahead of print]30(17):

Development and Validation of an LC-MS/MS Method for the Simultaneous Determination of Alprazolam, Bromazepam, Clonazepam, Diazepam and Flunitrazpam in Human Urine and Its Application to Samples from Suspected Drug Abusers.

Husein Kamal, Varun Gandhi, Lina Akil, Naser F Al-Tannak, Nicholas J W Rattray, Ibrahim Khadra.

  A simple and reliable method was developed using LC-MS/MS to quantify alprazolam, bromazepam, clonazepam, diazepam, and flunitrazepam in clinical samples. This method was validated for the simultaneous determination of alprazolam, bromazepam, clonazepam, diazepam, and flunitrazepam. It was applied to human urine samples collected from people suspected of drug abuse in the Kuwaiti region. Formic acid in water and acetonitrile was used in mobile phase with a gradient mode of elution using C18 reverse-phase column. The instrument was operated in a positive mode with an electrospray ionization source using multiple reaction monitoring. For sample extraction, the liquid-liquid extraction technique was used. The method was validated for limit of detection, limit of quantitation, selectivity, linearity, accuracy, and precision. The concentration for limit of quantitation was 6.0 ng/mL, the linearity ranged from 2.0 to 300 ng/mL for each of the analytes, and the r2 values were ≥0.99. The accuracy was found to be within a range of 80-120% and precision had a %RSD of ≤15% for each of the analytes. The method was applied to 48 urine samples collected from those suspected of drug abuse by the Toxicology Department of the General Department of Criminal Evidence, Kuwait, and alprazolam, bromazepam, clonazepam, diazepam and flunitrazepam were identified commonly in the samples. The overall drug positivity rate obtained considering 48 samples was 93.75%. Based on these results and successful determination of alprazolam, bromazepam, clonazepam, diazepam and flunitrazepam in human urine samples from those suspected of drug abuse, this method is deemed to be suitable for its routine analysis.

Keywords:  LC-MS/MS; benzodiazepines; diazepam; drug abuse; urine analysis

DOI:  https://doi.org/10.3390/molecules30173451
Anal Methods. 2025 Sep 09.

Simultaneous determination of ten sweeteners in soybean products using PRiME HLB purification combined with ultra-high-performance liquid chromatography-tandem mass spectrometry.

Yi Bao, Jinping Guo, Jinming Wang, Dan Li, Zhuo Lv, Xu Zhang, Xue Yang, Zeyue Gao, Lanying Zhou.

A method for determination of ten kinds of sweeteners in soybean products by multi-plug filtration cleanup (m-PFC) combined with ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was established. The sample was extracted with acetonitrile (containing 1% formic acid), degreased by using n-hexane liquid-liquid extraction and purified by solid phase extraction using an m-PFC column (Oasis PRiME HLB). The analytes were separated by using a Waters ACQUITY UPLC® BEH C18 (2.1 mm × 150 mm, 1.7 μm) column, and gradient eluted with a mixed solution of (5 mmol L-1 ammonium formate +0.1% formic acid) and acetonitrile. The mass spectrometric acquisition was performed by multiple-reaction monitoring (MRM) in both negative and positive ionization mode. Quantitative analysis was performed using an external standard method with matrix-matched calibration curves. Under optimal conditions, a total of ten target compounds were well separated within 10 min, and a good linearity was obtained in the concentration range of 5.00-500 μg L-1 with correlation coefficients greater than 0.99, and the limits of detection (LODs) and quantification (LOQs) for ACE-K, SAC and SCL were 25.0 and 50.0 μg kg-1; the limits of detection (LODs) and quantification (LOQs) for CYC, ASP, ALI, RBA, STV, ADV and NEO were 12.5 and 25.0 μg kg-1,respectively. The recoveries of the ten sweeteners in soymilk samples ranged from 76.9% to 115% at low, medium and high spiked levels (25.0-50.0 μg kg-1, 50.0-100 μg kg-1, and 250-500 μg kg-1), with precisions (RSD) in the range of 0.62-3.98%. This method is simple, rapid, accurate and sensitive, which greatly improves the efficiency of sample analysis and the accuracy of qualitative and quantitative analysis results of the target substances. It could meet the needs of quantitative analysis and qualitative screening of sweeteners in bulk soybean product samples, and provide technical support for rapid analysis of sweeteners in soybean products. It is of great significance for the analysis of trace components of sweeteners in soybean products.

DOI: https://doi.org/10.1039/d5ay00897b
Anal Chem. 2025 Sep 06.

Chemical Tagging with Mass Spectrometry Analysis for Sensitive Determination of Carboxylic Enantiomers in Hepatic Fibrosis.

Yu-Han Dai, Jun Zhang, Yi Gong, Yue Zhu, Chuanling Jiang, Chengjie Ma, Fei-Long Liu.

Carboxylic enantiomers are prevalent in living organisms and synthetic samples that exhibit important biological properties. The profiling of carboxylic enantiomers is beneficial for monitoring physiological states and further unraveling the metabolism mechanisms between carboxylic enantiomers and diseases. In this study, pairs of light and heavy isotope reagents, (S)-(3-aminopiperidin-1-yl) phenyl-methanone/d5-(S)-(3-aminopiperidin-1-yl) phenyl-methanone (APMA/d5-APMA), were synthesized and applied to tag the enantiomers of carboxylic metabolites and drugs. The tagging reagents of APMA and d5-APMA carry chiral amine groups that can efficiently and selectively react with the carboxyl group on carboxylic enantiomers. Upon the tagging strategy, pairs of carboxylic enantiomers showed satisfactory chromatographic performance on the conventional reversed-phase (RP) column, and the detection sensitivities of mass spectrometry (MS) analysis were also elevated. The obtained limits of detection (LODs) of 16 carboxylic enantiomers were in the range of 0.008-0.08 ng mL-1. With the developed method of APMA/d5-APMA tagging-assisted liquid chromatography-mass spectrometry (LC-MS) analysis, we successfully achieved the sensitive detection of carboxylic enantiomers in trace amounts of serum samples. The results showed that the levels of 6 carboxylic enantiomers in hepatic fibrosis serum presented significant alteration compared with normal serum samples. This proposed method provides great potential for uncovering the biological function of carboxylic enantiomers in the development of diseases.

DOI: https://doi.org/10.1021/acs.analchem.5c03449
J Chromatogr A. 2025 Aug 30. pii: S0021-9673(25)00671-5. [Epub ahead of print]1762 466327

Online solid-phase extraction coupled to liquid chromatography and tandem-mass spectrometry for the determination of glyphosate and other polar pesticide residues in plant commodities.

Eric Eichhorn, Walter Vetter, Michelangelo Anastassiades.

  The LC-MS/MS analysis of highly polar organophosphonate and -phosphinate pesticide residues such as glyphosate (Gly), N-acetyl-Gly, aminomethylphosphonic acid, glufosinate (Glu), N-acetyl-Glu, methylphosphinicopropionic acid, fosetyl, and ethephon remains a challenge, because matrix effects can strongly impair their determination. Here, we aimed to overcome such issues by means of an online SPE-LC-MS/MS method using ZrO2 (zirconia) as the adsorbent for these analytes. Extracts obtained with the widely employed Quick Polar Pesticides (QuPPe) method were first directed to the ZrO2 SPE column to trap the target analytes while the bulk of matrix compounds were removed. Initial direct linking of the ZrO2 SPE column with the tandem mass spectrometer (MS/MS) verified a full retention of the analytes, despite the presence of competing matrix compounds present in critical matrix extracts. The trapped analytes were released in backflush mode. The use of two HPLC pumps enabled the parallel rinsing of the ZrO2 SPE column during the separation of the analytes on the analytical HPLC column and their MS/MS quantification. Using this concept, the developed online SPE-LC-MS/MS method proved to be sensitive with moderate and generally comparable matrix effects for five plant-based commodities, including rather complex matrices such as soy flour. After successfully validating the method in accordance with Document No. SANTE/11312/2021 down to 0.01 mg/kg for each analyte, the method was applied to 172 routine samples of plant origin. Overall, the online SPE-LC-MS/MS method turned out to be a promising alternative for the analysis of highly polar organophosphonate and -phosphinate pesticide residues in complex matrices.

Keywords:  Online SPE-LC-MS/MS; Organophosphinate; Organophosphonate; Polar pesticide; Zirconia

DOI:  https://doi.org/10.1016/j.chroma.2025.466327
Anal Chim Acta. 2025 Nov 01. pii: S0003-2670(25)00942-0. [Epub ahead of print]1373 344548

Elaboration of trapping conditions on zirconia for the online SPE-LC-MS/MS analysis of glyphosate and other polar organophosphonate and -phosphinate pesticide residues in plant-based food extracts.

Eric Eichhorn, Walter Vetter, Michelangelo Anastassiades.

   BACKGROUND: Previous studies involving cleanup via conventional solid-phase extraction (SPE) materials to overcome matrix effects for the polar organophosphonate and -phosphinate pesticides glyphosate, glufosinate, ethephon, fosetyl, and their various metabolites often showed limitations due to the existence of various matrix compounds in plant commodities with similar polarity. To overcome existing drawbacks, we utilized the unique selectivity provided by metal oxides as SPE materials. These were exploited in a novel automated online SPE-LC-MS/MS method which allowed analyte-specific trapping in the presence of excessive amounts of matrix compounds as typically contained in extracts of the Quick Polar Pesticides (QuPPe) method.
RESULTS: For the purpose of this study, we combined the analytes with high levels of ten food-relevant matrix compounds based on the highest levels encountered in various food commodities. Initial comparisons indicated a quantitative trapping of all the considered analytes under these quasi worst-case scenarios on zirconia (ZrO2) but not on titania (TiO2). The impact of different eluent additives (formic acid and acetic acid) and organic solvents (acetonitrile and methanol) were studied in terms of efficiency, selectivity and robustness. Finally, 50 mmol/L formic acid in water/methanol (50/50, v/v) was employed during the analyte trapping on the zirconia SPE column. Sugars and certain anions such as chloride and nitrate could be effectively removed, while matrix compounds such as organic acids with an affinity towards zirconia, similar to the analytes, were also trapped.
SIGNIFICANCE: The insights of the developed online SPE-LC-MS/MS method provided a viable strategy when developing online SPE approaches, as the presented setup enabled a flexible monitoring of all SPE steps within one run during method development without changes in the configuration. The ZrO2 SPE material offered a robust tool for future implementation in a fully developed and automated online-SPE-LC-MS/MS method for the routine analysis of polar organophosphonate and -phosphinate pesticide residues.

Keywords:  Glyphosate; Online solid-phase extraction (SPE); Organophosphorus; Polar pesticide analysis; Tandem mass spectrometry; Transition metal oxide

DOI:  https://doi.org/10.1016/j.aca.2025.344548
J Chromatogr A. 2025 Sep 03. pii: S0021-9673(25)00684-3. [Epub ahead of print]1761 466340

Impact of injection solvent composition on 90 pesticides by LC-MS/MS: A data-driven framework for initial method development.

Abderrahim Eddahby, Abdelkarim Chahine, Lahcen Hssaini.

  The composition of the injection solvent is a critical, yet often underestimated, parameter in liquid chromatography-tandem mass spectrometry (LC-MS/MS). This study systematically evaluates the influence of injection solvent on the analysis of 90 pesticides by comparing mixtures of acetonitrile (ACN) with water and buffered mobile phase A (5 mM ammonium formate, 0.1% formic acid) across various ratios (10/90 to 50/50, v/v). The investigation, conducted using solvent-based standards, explicitly focuses on chromatographic and ionization effects in the absence of sample matrix. Results reveal distinct, polarity-dependent response patterns. Early-eluting, polar compounds (e.g., methamidophos) demonstrated up to a 14-fold signal enhancement in highly aqueous solvents (10/90 ACN/water), attributed to improved on-column focusing. Conversely, late-eluting, non-polar analytes (e.g., spinosad) required higher organic content (50/50 ACN/water) to ensure solubility and maximize response. A 30/70 ACN/aqueous ratio emerged as a robust compromise for most mid-polarity compounds. ANOVA confirmed that solvent ratio significantly impacts MS response (p < 0.001). While matrix effects were not within the scope of this study, the research provides a foundational framework and practical guidelines for selecting an optimal injection solvent during initial method development, thereby enhancing the sensitivity and chromatographic integrity of multi-residue pesticide analyses.

Keywords:  Acetonitrile solvent mixtures; Ionization enhancement; LC-MS/MS; Mobile phase optimization; Pesticide residue analysis

DOI:  https://doi.org/10.1016/j.chroma.2025.466340
Drug Metab Rev. 2025 Sep 11. 1-60

Analytical Techniques for Methyldopa and Metabolites: A Comprehensive Review.

Hemn A H Barzani, Seerwan Hamadameen Sulaiman, Rebaz Anwar Omer, Ali Hussein Mer, Hoshyar Saadi Ali.

  Methyldopa, a centrally acting α2-adrenergic agonist, remains a key antihypertensive drug, particularly prescribed for pregnant and renal-impaired patients. Its clinical significance has led to extensive research aimed at developing reliable analytical methods for its accurate, sensitive, and selective determination in pharmaceutical formulations and biological matrices. Relevant literature was retrieved from Scopus, Web of Science, ScienceDirect, PubMed, and Google Scholar, restricted to English-language publications. This review critically examines the diverse analytical approaches used for Methyldopa quantification, outlining their principles, advantages, limitations, and applicability in both advanced and resource-limited settings. Chromatographic methods, especially high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS/MS), remain the most robust techniques, offering excellent sensitivity (LOD: 10-50 ng/mL for HPLC; as low as 0.7-15 ng/mL for LC-MS/MS) with rapid analysis times. While LC-MS/MS provides superior detection, it is limited by high costs and technical expertise requirements. Electrochemical methods, particularly voltammetry, stand out for their affordability, rapid analysis, and feasibility in decentralized laboratories, achieving LOD values as low as 0.01-0.05 µM. Spectrophotometric approaches, primarily UV-Vis, remain the simplest and most cost-effective options, making them useful for routine quality control, though with reduced selectivity and higher detection limits. Key analytical challenges include Methyldopa's low concentration in biological fluids, chemical instability, and matrix interferences. This review provides a comparative evaluation of chromatographic, spectrophotometric, and electrochemical techniques, emphasizing the need for portable, low-cost platforms to expand accessibility in therapeutic monitoring. Overall, it offers critical insights for advancing Methyldopa analysis and improving clinical management in diverse healthcare settings.

Keywords:  Bioanalysis; Drug analysis; Electrochemical analysis; High-performance liquid chromatography (HPLC); Hypertension; Methyldopa; Spectrophotometry; Voltammetry

DOI:  https://doi.org/10.1080/03602532.2025.2560487
Nat Protoc. 2025 Sep 08.

A versatile toolkit for drug metabolism studies with GNPS2: from drug development to clinical monitoring.

Jun Sang Yu, Young Beom Kwak, Kyung Hwa Kee, Mingxun Wang, Dong Hyun Kim, Pieter C Dorrestein, Kyo Bin Kang, Hye Hyun Yoo.

Metabolism is a fundamental process that shapes the pharmacological and toxicological profiles of drugs, making metabolite identification and analysis critical in drug development and biological research. Global Natural Products Social Networking (GNPS) is a community-driven infrastructure for mass spectrometry data analysis, storage and knowledge dissemination. GNPS2 is an improved version of the platform offering higher processing speeds, improved data analysis tools and a more intuitive user interface. Molecular networking based on tandem mass spectrometry spectral alignments, combined with other tools in the GNPS2 analysis environment, enables the discovery of candidate drug metabolites without prior knowledge, even from complex biological matrices. This protocol represents an extension of a previously established protocol for fundamental molecular networking in GNPS, with a specific focus on metabolism studies. This article uses the example of the drug sildenafil to identify candidate metabolites obtained from liquid chromatography-quadrupole time-of-flight mass spectrometry analysis of liver microsomal fractions and mice plasma to guide the reader through a step-by-step process consisting of five GNPS2-based analytical workflows. It demonstrates how the tools in GNPS2 can be used not only to identify candidate drug metabolites from in vitro studies but also to evaluate the translational relevance of these in vitro findings to humans by using reverse metabolomics. We provide a step-by-step analytical approach based on published studies to showcase how GNPS2 can be effectively applied in drug metabolism studies.

DOI: https://doi.org/10.1038/s41596-025-01237-6
Anal Chem. 2025 Sep 08.

De-MSI: A Deep Learning-Based Data Denoising Method to Enhance Mass Spectrometry Imaging by Leveraging the Chemical Prior Knowledge.

Lei Guo, Chengyi Xie, Xin Diao, Thomas Ka Yam Lam, Yanhui Zhong, Yanyan Chen, Jingjing Xu, Xiangnan Xu, Xiangyu Zhu, Zhuang Xiong, Shangyi Luo, Jianing Wang, Jiyang Dong, Zongwei Cai.

Mass spectrometry imaging (MSI) is a label-free technique that enables the visualization of the spatial distribution of thousands of ions within biosamples. Data denoising is the computational strategy aimed at enhancing the MSI data quality, providing an effective alternative to experimental methods. However, due to the complex noise pattern inherent in MSI data and the difficulty in obtaining ground truth from noise-free data, achieving reliable denoised images remains challenging. In this study, we introduce De-MSI, a novel deep learning-based method specifically developed for denoising MSI data without ground truth. The core concept of De-MSI involves constructing the reliable training data set by leveraging prior knowledge of mass spectrometry from the noisy MSI data, followed by training a deep neural network to improve the data quality by removing the noise from the original images. De-MSI has demonstrated superior performance in improving data quality over the commonly used methods when applied to MALDI-acquired mouse fetus data sets on visual inspection. Quantitative evaluations further confirm its superiority, with De-MSI achieving a mean PSNR of 18.93 and a mean SSIM of 0.74 across all ion images. The ability of De-MSI to enhance data quality in high-resolution MSI data sets is confirmed using the mouse brain data set at a pixel size of 5 μm. Additionally, its application to denoise rat brain data sets using the DESI technique showcases its adaptability across different ionization methods. The proposed model holds significant promise as a vital tool for the efficient analysis and interpretation of MSI data.

DOI: https://doi.org/10.1021/acs.analchem.5c02946
J Am Soc Mass Spectrom. 2025 Sep 11.

SLIM Ion Mobility-Based Analysis of Low Molecular Weight Explosives.

Heidi M Sabatini, Christopher D Chouinard.

  The detection and differentiation of explosive compounds remain critical components of security applications and forensic work due to the potential complexity of samples and presence of isomeric compounds. Standalone ion mobility spectrometry (IMS) has been used in security screening for decades, useful for its ability to rapidly separate gas-phase ions based on differences in their size, shape, and charge. More recently developed high-resolution ion mobility-mass spectrometry (HRIM-MS) methods incorporate higher resolving power with accurate mass measurements to provide improved isomer separations and identification of unknowns. This work utilizes a novel Structures for Lossless Ion Manipulations (SLIM) ion mobility platform featuring a rounded turn design, which enhances the transmission of low-mass explosive compounds using helium buffer gas. Using negative mode atmospheric pressure chemical ionization (APCI), we demonstrate separation of isomeric nitroaromatic compounds such as 2,4- vs 2,6-dinitrotoluene (2,4-/2,6-DNT) and 2-amino-4,6- vs 4-amino-2,6-DNT. The rounded turn SLIM design significantly improved ion transmission efficiency over the traditional 90° turn system, especially for these low m/z analytes. With this, we demonstrate the ability of SLIM HRIM-MS to combine mobility separations, accurate mass, and isotopic patterns for improved separation and identification of isomeric explosives.

Keywords:  Explosives; Ion Mobility-Mass Spectrometry; Structures for Lossless Ion Manipulations (SLIM)

DOI:  https://doi.org/10.1021/jasms.5c00268
Anal Chem. 2025 Sep 11.

A New Approach to Large Multiomics Data Integration.

Alex Dexter, Spencer A Thomas, Rory T Steven, Kenneth N Robinson, Adam J Taylor, Efstathios A Elia, Chelsea Nikula, Andrew D Campbell, Yulia Panina, Arafath K Najumudeen, Bin Yan, Piotr Grabowski, Gregory Hamm, John Swales, Aurelien Tripp, George Poulogiannis, Mariia O Yuneva, Simon Barry, Richard J A Goodwin, Owen J Sansom, Zoltan Takats, Josephine Bunch.

Data reduction and data mining are common practices for handling large-scale data from wide-ranging sources, but high-dimensional omics and imaging data sets present difficult challenges for feature extraction and data mining due to the large number of features that cannot be simultaneously examined. The sample numbers and variables in these methods are constantly growing as new technologies are developed, and computational analysis needs to evolve to keep up with growing demand. In recent years, there has been a rapid uptake of nonlinear dimensionality reduction via methods such as t-distributed stochastic neighbor embedding and uniform manifold approximation and projection. These approaches have revolutionized our ability to visualize and interpret high-dimensional data and have rapidly become preferred methods for analysis of data sets containing an extremely high number of variables. Further to this is the emerging interest in combining information from multiple omics sources to gain a more holistic view of systems biology. Current state-of-the-art algorithms can perform data mining, visualization, and classification on routine data sets but struggle when data sets grow above a certain size. We present a new approach to large and multiomic data integration to extract, mine, and integrate large multiomics data sets that were previously considered prohibitively large. Here, we demonstrate the use of deep learning on subsampled nonlinear dimensionality reduction using t-SNE and UMAP to extract features from large complex data sets including mass spectrometry imaging and chromosome conformation capture. We then go on to demonstrate how this method can be used to learn embeddings from the fusion of different omics data, allowing metabolomics data to be projected into a reduced transcriptomics representation.

DOI: https://doi.org/10.1021/acs.analchem.5c01812
Biomed Chromatogr. 2025 Oct;39(10): e70217

Metabolic Stability and Comprehensive Metabolite Profiling of Chrysotobibenzyl in Human Liver Microsomes and Hepatocytes Employing UPLC-MS/MS and UPLC-Orbitrap-HRMS Analysis.

Xuanwei Liu, Junsheng Ge, Nana Zhao, Yeji Liang, Yu Liu, Xiaoman Wang, Lihua Tan.

  Chrysotobibenzyl, a bioactive ingredient from Dendrobium chrysotoxum, exhibits potent anti-tumor activity. However, its metabolic profiles remain unelucidated. This study aimed to disclose the metabolic fates of chrysotobibenzyl using human liver fractions. In vitro metabolism of chrysotobibenzyl was assessed using human liver microsomes and hepatocytes. The concentration of unchanged parent compound was quantified using a validated UPLC-MS/MS method. Metabolite profiling was achieved by Q-Exactive Orbitrap HRMS combined with Compound Discoverer software using a mass defect filtering approach, with structures characterized by accurate mass measurement and fragmentation pattern interpretation. Chrysotobibenzyl exhibited poor metabolic stability in human liver microsomes (t1/2: 16.24 min) and hepatocytes (t1/2: 44.35 min). Totally, 36 metabolites were identified, comprising 19 phase I metabolites, 10 glucuronide conjugates, and seven GSH adducts. Using reference standards, M22, M25, M27, and M28 were unambiguously identified as moscatilin, chrysotoxine, erianin, and crepidatin, respectively. The detection of GSH conjugates indicated the formation of reactive metabolites, including ortho-quinone and quinone-methide intermediates. This study demonstrates the effectiveness of UPLC-MS/MS and UPLC-Orbitrap-HRMS platforms for metabolic profiling. Metabolic pathways include demethylation, hydroxylation, dehydrogenation, glucuronidation, and GSH conjugation. These findings provide critical insights into the metabolism of chrysotobibenzyl in humans, enhancing our understanding of its biological activity.

Keywords:  chrysotobibenzyl; dendrobium; metabolic stability; metabolite characterization

DOI:  https://doi.org/10.1002/bmc.70217