bims-metlip 2025-07-13 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2025–07–13
25 papers selected by
Sofia Costa, Matterworks

Bacterial biofilm sample preparation for spatial metabolomics.
SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation.
Triple labeling of metabolites for metabolome analysis (TLEMMA): a stable isotope labeling approach for metabolite identification and network reconstruction.
A novel immunoprecipitation-based targeted liquid chromatography-tandem mass spectrometry analysis for accurate determination for copeptin in human serum.
LC-MS/MS Assay for Simultaneous Quantification of Dual-Targeting 1,5-Diaryl-1,2,4-Triazole Sulfonamides (WA11-13) in Human Plasma.
Simple, Sensitive and Reproducible High-performance Liquid Chromatographic Method for Determination of Mixed Tocotrienol in Blood Plasma using Fluorescent Detection.
Mechanism-based perspective on metal ion-induced signal instability and development of a robust LC-MS/MS method for trace quantification of hetrombopag in plasma.
MAMSI: Integration of Multiassay Liquid Chromatography-Mass Spectrometry Metabolomics Data Using Multiview Machine Learning.
Comparative evaluation of cerebral tissue pretreatment strategies for metabolomics using UHPLC-high-resolution mass spectrometry.
A Novel UPLC-MS/MS Method for Detecting Simnotrelvir in Rat Plasma and Its Application for Pharmacokinetics.
Efficient Quantification of Tacrolimus in Rat Plasma With Ultra-High Performance LC-Q-Orbitrap MS: A Precision Pharmacokinetic Analysis Tool.
Paper spray and direct mushroom spray mass spectrometry methods for the analysis of psycho-neurological disorder toxins.
Liquid chromatography-tandem mass spectrometry methods for clinical quantitation of antibiotics.
Critical Method Parameters to Evaluate When Developing a Method Using a Laser Diode Thermal Desorption (LDTD) Coupled to a Mass Spectrometer.
Assessment of Variable Traveling Wave Profiles for Small-Molecule Applications in Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS).
Determination of per- and polyfluoroalkyl substances in tissue using QuEChERS extraction followed by novel enhanced matrix removal mixed-mode passthrough cleanup with LC-MS/MS detection.
A Supercritical Fluid Chromatographic Method for the Determination and Separation of Boronic Acids.
Method development for correlating lipid molecular information with anatomy in C. elegans.
Quantitative quadrupolar NMR (qQNMR) determination of taurine in undiluted human urine samples using 1D and 2D 33S NMR.
Liquid chromatography-mass spectrometry approach for characterizing sucrose isomers in complex mono-floral honey.
Transformer-based Deep Learning for Glycan Structure Inference from Tandem Mass Spectrometry.
Rapid Screening of 25 Environmental Hormones in Aquatic Products Using QuEChERS-Combined With Dispersive Liquid-Liquid Microextraction Based on Solidification of Floating Organic Droplet Coupled With UHPLC-Q/Orbitrap HRMS.
The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration.
Orbitrap noise structure and method for noise unbiased multivariate analysis.
Simultaneous analysis of organic and inorganic explosive traces by online two-dimensional liquid chromatography.

Analyst. 2025 Jul 08.

Bacterial biofilm sample preparation for spatial metabolomics.

Joenisse M Rosado-Rosa, Jonathan V Sweedler.

Spatial metabolomics using mass spectrometry imaging (MSI) has become an important approach to study the surface of biological systems. MSI can probe bacterial metabolic processes through the direct analysis of bacterial colonies. In this review, we explore recent advancements made for bacterial metabolomics of primary and secondary metabolites using MSI, focusing on improvements in agar-based sample preparation and the use of membranes for improved sample preparation. The application of derivatization agents on bacterial samples enhances select metabolite signals and can aid analyte identification. Implementing dual imaging or multi-omics techniques also aids in identifying analytes and elucidating metabolic pathways active during the host-microbe interactions. Finally, we explore improvements towards robust three-dimensional protocols for whole colony MSI analysis. These advances enhance MSI analysis of bacterial samples and pose promising avenues for future studies.

DOI: https://doi.org/10.1039/d5an00466g
Brief Bioinform. 2025 Jul 02. pii: bbaf333. [Epub ahead of print]26(4):

SingleFrag: a deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation.

Maribel Pérez-Ribera, Muhammad Faizan-Khan, Roger Giné, Josep M Badia, Alexandra Junza, Oscar Yanes, Marta Sales-Pardo, Roger Guimerà.

  Metabolite and small molecule identification via tandem mass spectrometry (MS/MS) involves matching experimental spectra with prerecorded spectra of known compounds. This process is hindered by the current lack of comprehensive reference spectral libraries. To address this gap, we need accurate in silico fragmentation tools for predicting MS/MS spectra of compounds for which empirical spectra do not exist. Here, we present SingleFrag, a novel deep learning tool that predicts individual fragments separately, rather than attempting to predict the entire fragmentation spectrum at once. Our results demonstrate that SingleFrag surpasses state-of-the-art in silico fragmentation tools, providing a powerful method for annotating unknown MS/MS spectra of known compounds. As a proof of concept, we successfully annotate three previously unidentified compounds frequently found in human samples.

Keywords:  Graph neural networks; In silico fragmentation; MS/MS; Machine learning; Metabolite

DOI:  https://doi.org/10.1093/bib/bbaf333
Plant J. 2025 Jul;123(1): e70333

Triple labeling of metabolites for metabolome analysis (TLEMMA): a stable isotope labeling approach for metabolite identification and network reconstruction.

Yonghui Dong, Liron Feldberg, Yi Wang, Uwe Heinig, Ilana Rogachev, Asaph Aharoni.

  Metabolite identification remains a significant challenge in mass spectrometry (MS)-based metabolomics research. To address this issue, we combined a triple-labeled precursor-based isotope tracing approach (TLEMMA) with high-resolution liquid chromatography-MS for metabolite identification and metabolic network construction. As a demonstration, we fed duckweed (Spirodela polyrhiza) with four forms of phenylalanine (Phe) including unlabeled Phe, Phe-5H2, Phe-8H2, and Phe-13C9 15N1. The distinctive isotopic pattern obtained from MS spectra greatly facilitated data processing, enabling comprehensive extraction of all Phe-derived metabolites. Importantly, the labeling pattern allowed efficient metabolite identification by significantly reducing the number of structural and positional isomers. Using this approach, 47 phenylalanine-derived metabolites were putatively identified. To further evaluate the efficiency of metabolite identification in relation to the number of differently labeled precursors used, we compared the number of filtered candidates based solely on the labeling patterns obtained from unlabeled, single, dual, and triple isotope-labeled precursor tracing experiments. On average, TLEMMA eliminates the number of false candidates by 99.1% compared with unlabeled samples, 95% compared with single isotope-labeled samples, and 66.7% compared with dual isotope-labeled samples. This significant reduction in the number of false positives, along with the ability to identify previously unreported metabolites, demonstrates the power of TLEMMA in advancing the field of metabolomics and metabolic network reconstruction.

Keywords:  metabolite identification; plant metabolomics; stable isotope labeling; technical advance

DOI:  https://doi.org/10.1111/tpj.70333
Clin Chem Lab Med. 2025 Jul 10.

A novel immunoprecipitation-based targeted liquid chromatography-tandem mass spectrometry analysis for accurate determination for copeptin in human serum.

Danni Mu, Xiaoli Ma, Yichen Ma, Danchen Wang, Yutong Zou, Ying Zhu, Jian Zhong, Dandan Sun, Yicong Yin, Yumeng Gao, Yuemeng Li, Shi Chen, Huijuan Zhu, Songlin Yu, Ling Qiu, Xinqi Cheng.

   OBJECTIVES: Copeptin, a stable and simple-to-measure surrogate marker for arginine vasopressin (AVP), demonstrates excellent clinical values, particularly in diagnosing polyuria-polydipsia syndromes. However, conventional immunoassay methods are limited and lack comparability. Our aim was to establish a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying copeptin in human serum.
METHODS: Copeptin was extracted from serum using immunoprecipitation, digested with trypsin, and prepared using anion exchange solid-phase extraction before LC-MS/MS detection. The analytical performance was validated in accordance with current guidelines. The method was compared to an immunofluorescent assay on the B.R.A.H.M.S platform.
RESULTS: The LC-MS/MS method had a runtime of 8.5 min. The within-run precision ranged from 5.2 to 12.1 %, and total coefficients of variation ranged from 8.1 to 13.5 %. Copeptin quantitation showed linearity within the range of 5-1,000 pg/mL, with a limit of detection of 2.5 pg/mL. Recovery rates ranged from 95.2 to 103.1 %, and no significant matrix effect was observed with internal standard correction. The LC-MS/MS method had a good consistency with the immunoassay (r=0.926, slope=0.989). The reference interval for healthy individuals was 3.66-58.25 pg/mL.
CONCLUSIONS: We demonstrated the accuracy and reliability of this targeted LC-MS/MS method for quantifying copeptin. This innovative application showed satisfactory precision, a wide linear range, and a low limit of detection. Clinical studies are anticipated to be conducted to assess diagnostic accuracy using this method.

Keywords:  biomarker; copeptin; immunoprecipitation; liquid chromatography–tandem mass spectrometry; quantitation

DOI:  https://doi.org/10.1515/cclm-2025-0022
Biomed Chromatogr. 2025 Aug;39(8): e70165

LC-MS/MS Assay for Simultaneous Quantification of Dual-Targeting 1,5-Diaryl-1,2,4-Triazole Sulfonamides (WA11-13) in Human Plasma.

Fawzy A Elbarbry, Bethany Hecker, Michael J Espiritu, Ahmed E Elsawi, Wagdy M Eldehna.

  We recently designed and synthesized novel dual-targeting anticancer 1,5-diaryl-1,2,4-triazole-tethered sulfonamides. Among them, WA11-13 showed promising carbonic anhydrase and VEGFR-2 inhibitory activity. This study presents a validated, sensitive LC-MS/MS assay for quantifying these compounds in human plasma. Such assay would be very important for future preclinical studies and therapeutic drug monitoring. After protein precipitation with acetonitrile, analytes and the internal standard (carbamazepine) were separated on a Phenomenex Kinetex C18 column using binary gradient elution. The mobile phase was 0.1% formic acid in water and acetonitrile (95:5, v/v) at 0.7 mL/min. Total run time was under 6 min. Detection used an API 3500 triple quadrupole mass spectrometer with electrospray ionization in positive mode. Quantification relied on multiple reaction monitoring for high sensitivity and specificity. The method was fully validated per FDA guidelines, showing acceptable linearity, accuracy, precision, selectivity, and stability. Linearity was observed in the ranges of 2.5-750 ng/mL for WA11, 25-1000 ng/mL for WA12, and 50-1000 ng/mL for WA13. The method was successfully applied to spiked human plasma, supporting its potential for therapeutic drug monitoring. Validation confirms the assay's high sensitivity, accuracy, and precision, making it suitable for future preclinical and clinical investigations of these investigational anticancer agents.

Keywords:  LC–MS/MS; antitumor; bioanalytical validation; carbonic anhydrase inhibitors; human plasma; tandem mass

DOI:  https://doi.org/10.1002/bmc.70165
J Chromatogr Sci. 2025 Jun 10. pii: bmaf041. [Epub ahead of print]63(6):

Simple, Sensitive and Reproducible High-performance Liquid Chromatographic Method for Determination of Mixed Tocotrienol in Blood Plasma using Fluorescent Detection.

Teong G Thor, Song T Goh, Kah H Yuen, Jacqueline K K Mark, Siok Y Chan.

A simple, sensitive and reproducible high-performance liquid chromatographic (HPLC) method with fluorescence detection was developed and validated for the simultaneous quantification of mixed tocotrienols (α-, γ- and δ-) in human plasma. The method involves a straightforward sample preparation step, where plasma samples are deproteinized using a mixture of acetonitrile and tetrahydrofuran (3:2, v/v), followed by direct injection into the HPLC system. Separation was achieved using a methanol mobile phase at a flow rate of 1.5 mL/min, with fluorescence detection at excitation and emission wavelengths of 296 nm and 330 nm, respectively. The method demonstrated excellent linearity over concentration ranges of 12.7 ng/mL to 2.54 μg/mL for α-tocotrienol, 19.2 ng/mL to 3.84 μg/mL for γ-tocotrienol and 4.6 ng/mL to 0.923 μg/mL for δ-tocotrienol, with quantification limits of 12.7 ng/mL, 19.2 ng/mL and 4.6 ng/mL, respectively. Recovery rates ranged from 85.0% to 111.2%, and both intra-day and inter-day precision showed relative standard deviations below 15%. The method was validated for accuracy, precision and stability under various conditions, including freeze-thaw cycles and long-term storage. This HPLC method offers a rapid, sensitive and reliable approach for quantifying tocotrienols in human plasma, making it suitable for preclinical and clinical studies, particularly in pharmacokinetic and bioavailability research.

DOI: https://doi.org/10.1093/chromsci/bmaf041
J Pharm Biomed Anal. 2025 Jul 03. pii: S0731-7085(25)00390-5. [Epub ahead of print]265 117049

Mechanism-based perspective on metal ion-induced signal instability and development of a robust LC-MS/MS method for trace quantification of hetrombopag in plasma.

Jiangbin Han, Lijuan Zhai, Jie Wang, Biying Dai, Huiyue Lu, Jiao Chen, Xiaoli Wang, Yuyu Wu, Wen Qian.

  Hetrombopag (Hengqu®) is an oral nonpeptide thrombopoietin receptor agonist for the treatment of thrombocytopenia and aplastic anemia. Research on the pharmacokinetic behavior is very important, but accurate quantification of metal-sensitive hetrombopag in biological specimens is a challenging analytical problem. In view of the presence of trace metals from a variety of sources, such as chromatographic system, containers, and the mass spectrometry spray needle, which can contribute to poor peak shape, tailing, and diminished recovery of compound. To ameliorate these problems, different solvent additives, mobile phase, containers and precipitant reagents were investigated to reduce the negative effects. In the present study, a robust, selective, and sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the determination of hetrombopag in dog plasma was developed based on the dual strategies: (1) 6 % perchloric acid in acetonitrile eliminates metal ion adsorption in storage containers, and (2) 0.01 % trifluoroacetic acid (TFA) in the mobile phase suppresses chelation in chromatographic systems. These two solvents are essential requirements for ensuring stable analytical signals. This method employed an InfinityLab Poroshell 120 EC-C18 column (4.6 ×50 mm, 2.7 μm, Agilent) with a gradient system comprising 0.01 % trifluoroacetic acid with 10 mM ammonium formate (phase A) and a mixture of H2O: methanol: isopropanol (1:10:10, v/v/v) containing 0.01 % trifluoroacetic acid and 10 mM ammonium formate (phase B). The column temperature of 50℃ and the addition of isopropanol were beneficial for the separation of interfering peaks and target analyte peaks in plasma. The method exhibits excellent linearity over 3 orders of magnitude. The method achieved a lower limit of quantification (LLOQ) of 0.10 ng/mL using only 50 μL of plasma, with precision (RSD ≤ 8.83 %) and accuracy (88.4-102.2 %) within acceptable limits. The method was applied to determine the plasma concentration of hetrombopag in eight male beagle dogs after each administration of three 2.5 mg hetrombopag tablets. The analytical methodology described in the present work should be useful in the future work aiming to establish a model relating metal-sensitive other compounds.

Keywords:  HPLC-PDA; Hetrombopag; LC−MS/MS; Metal-sensitive; Pharmacokinetics

DOI:  https://doi.org/10.1016/j.jpba.2025.117049
Anal Chem. 2025 Jul 10.

MAMSI: Integration of Multiassay Liquid Chromatography-Mass Spectrometry Metabolomics Data Using Multiview Machine Learning.

Lukas Kopecky, Caroline J Sands, María Gómez-Romero, Shivani Misra, Elizabeth J Want, Timothy M D Ebbels.

Liquid chromatography-mass spectrometry (LC-MS) is a commonly used analytical technique in untargeted metabolomics. However, the diverse chemical and physical properties of metabolites often require the use of several different analytical assays for broad metabolome coverage. Conventionally, each assay is analyzed separately, but this fails to capture interassay relationships, making multiassay biomarker discovery and data interpretation difficult. Here we propose a workflow to integrate multiassay metabolomics data, designed to enable biomarker discovery and elucidation of unknown metabolites. We employ a multiblock-partial least-squares model (MB-PLS) coupled with multiblock variable importance in projection to estimate the importance of predictors to the outcome variable. Then we cluster the selected predictors and compare them to groups defined by their structural properties based on retention time and mass-to-charge ratio. To demonstrate and evaluate the approach, we used three multiassay data sets predicting biological sex, Alzheimer's disease status, and blood bilirubin levels as the outcomes of interest. The MB-PLS models outperformed single-assay models in both classification and regression tasks, indicating that modeling interblock relationships enabled an improved estimate of phenotypic outcome. Additionally, the MB-PLS models shed valuable insight into each data block's contribution to the predicted outcome. Our workflow enabled us to determine a set of potential cross-assay biomarkers. Following putative annotation, the majority of these and their signs of association agreed with results previously reported in the literature. Our workflow has the potential to benefit the metabolomics community and beyond as it offers interpretable integrative analysis of multiassay LC-MS data and facilitates discovery of potential biomarkers.

DOI: https://doi.org/10.1021/acs.analchem.5c01327
J Neurosci Methods. 2025 Jul 04. pii: S0165-0270(25)00168-2. [Epub ahead of print]422 110524

Comparative evaluation of cerebral tissue pretreatment strategies for metabolomics using UHPLC-high-resolution mass spectrometry.

Fang Guo, Xiaoxue Zhou, Yudie Ning, Tingli Qv, Jieping Lv, Tao Wang, Zhiwen Wei.

   BACKGROUND: The cerebrum, as the most complex human organ, contains diverse metabolites vital for understanding brain functions, diseases, drug effects, and addiction. Its liquefiable nature makes swift preparation crucial to preserve metabolic profiles, with physical homogenization needed to release metabolites. To determine the optimal preparation procedures for cerebrum samples for high-resolution mass spectrometry in metabolomics, we evaluated four homogenization techniques and three extraction protocols using UHPLC-HRMS.
NEW METHOD: A combination of dry grinding and monophasic extraction was identified as an optimized sample preparation approach for cerebrum metabolomics.
RESULTS: The number of feature peaks, coefficient of variation (CV) of peak areas, and peak areas were compared to evaluate the coverage, reproducibility, and sensitivity of the methods. The dry grinding method detected the most feature peaks among four methods of homogenization, and the peak areas obtained were superior to other homogenization methods. In terms of extraction methods, there was no significant difference in peak areas (except for tyrosine) between monophasic and two-step extraction methods (p > 0.05), both of which were higher than the biphasic extraction method (p < 0.05). Additionally, the reproducibility of the monophasic extraction method was significantly better than the other two methods.
COMPARISON: The dry grinding and monophasic extraction approach demonstrated excellent compatibility with UHPLC-HRMS, offering broader metabolite coverage and superior performance compared to existing methods.
CONCLUSIONS: The dry grinding and monophasic extraction method is recommended for cerebrum metabolomics, providing enhanced metabolite coverage, reproducibility, and adaptability for high-resolution mass spectrometry studies.

Keywords:  Cerebrum; Metabolomics; Pretreatment; UPLC Orbitrap Q Exactive Plus

DOI:  https://doi.org/10.1016/j.jneumeth.2025.110524
Biomed Chromatogr. 2025 Aug;39(8): e70162

A Novel UPLC-MS/MS Method for Detecting Simnotrelvir in Rat Plasma and Its Application for Pharmacokinetics.

Mengjie Xu, Binbin Yan, Manjie Lin, Qinghua Weng.

  Simnotrelvir is a commonly used antiviral agent. In this study, we aimed to establish a novel UPLC-MS/MS method to quantitatively determine simnotrelvir in rat plasma and its application for pharmacokinetic research. Protein precipitation was used to prepare rat plasma. Gradient elution with a flow rate of 0.4 mL/min was applied for the separation of simnotrelvir and nirmatrelvir (internal standard) on a Waters ACQUITY UPLC BEH C18 column (1.7 μm, 2.1 × 50 mm). The mobile phase consisted of methanol and water. The mass transition pairs for nirmatrelvir and simnotrelvir were m/z 500.3 → 110.3 and m/z 550.20 → 160.15, respectively. In the bioanalytical method, it exhibited a good linearity (5-5000 ng/mL). The accuracy and precision ranged from -6.0% to 14.8% and 1.1% to 13.2%, respectively. The recovery and matrix effect of simnotrelvir were acceptable. Additionally, this analytical method was successfully used in pharmacokinetics in rats after oral administration. Pharmacokinetic parameters suggested that after oral administration, simnotrelvir reached the peak at 4.00 ± 1.10 h with a Cmax value of 10376.02 ± 4301.78 ng/mL. The half-life of simnotrelvir was nearly 3 h. These results indicated that simnotrelvir was rapidly absorbed and cleared quickly in vivo.

Keywords:  nirmatrelvir; pharmacokinetics; rat; simnotrelvir

DOI:  https://doi.org/10.1002/bmc.70162
Biomed Chromatogr. 2025 Aug;39(8): e70164

Efficient Quantification of Tacrolimus in Rat Plasma With Ultra-High Performance LC-Q-Orbitrap MS: A Precision Pharmacokinetic Analysis Tool.

Xiao-Rong Zhang, Jia Yao, Teng-Fei Ma, Hao-Yu Chen, Heng-Ju Xu, Ying-Hui Ye, Li-Ying Zhai.

  The narrow therapeutic index of tacrolimus demands precise dose optimization to maintain therapeutic efficacy while minimizing toxicity, underscoring the necessity for reliable analytical techniques to accurately measure drug concentrations in biological matrices. In this study, we developed an ultrahigh-performance liquid chromatography coupled with quadrupole-orbitrap mass spectrometry method for quantifying tacrolimus in plasma. This approach employed an Acquity UPLC BEH C18 column, leveraging a gradient elution of methanol (A) and water with 0.1% formic acid (B) to ensure meticulous separation of tacrolimus and the internal standard, ascomycin. Operating in positive ionization mode, the system utilized full MS/dd-MS2 scans, capturing comprehensive data for heightened analytical accuracy and precision. The method demonstrated a broad linear range of 0.5 to 500 μg/L, with a low quantification limit of 0.5 μg/L. Notably, it achieved exceptional reproducibility and accuracy, with relative standard deviations and errors below 6%, complemented by consistent extraction efficiencies for tacrolimus at 84.78% to 97.15%. This study successfully showcases an advanced analytical platform for the meticulous quantification of tacrolimus, seamlessly integrating into pharmacokinetic investigations following a 1.2 mg/kg oral dose in rats. The method's deployment revealed its exceptional suitability for capturing intricate pharmacokinetic profiles, underscoring its value in preclinical drug disposition studies.

Keywords:  Orbitrap MS; UHPLC; pharmacokinetics; tacrolimus

DOI:  https://doi.org/10.1002/bmc.70164
Food Chem. 2025 Jun 28. pii: S0308-8146(25)02620-2. [Epub ahead of print]492(Pt 1): 145369

Paper spray and direct mushroom spray mass spectrometry methods for the analysis of psycho-neurological disorder toxins.

Wei Luo, Qiaolian Dai, Teris A van Beek, Han Zuilhof, Bo Chen, Zuohong Chen, Gert Ij Salentijn.

  Fast screening approaches based on paper spray ionization were developed to identify psycho-neurological disorders mushrooms. Directly spraying from mushroom tissue already allowed direct identification of muscarine, psilocin, and ibotenic acid within 2-3 min. For quantitative analysis of the more challenging ibotenic acid, a new anion-exchange modified paper spray tandem mass spectrometry (AEPS-MS/MS) method was established to increase selectivity and sensitivity. The developed method was benchmarked against HPLC-MS/MS (with detection limits of 0.009 μg mL-1) and could reach detection limits of 1.3 μg mL-1 for ibotenic acid spiked in mushroom extract, with acceptable accuracy (-14.0 % to +5.1 %) and precision (10.8 % to 18.0 %). In addition, the developed method was compared with solid-phase extraction coupled with PS-MS/MS (with detection limits of 2.8 μg mL-1). Finally, the AEPS-MS/MS was applied for the quantitative analysis of ibotenic acid in Amanita griseopantherina, matching results from HPLC-MS/MS.

Keywords:  HPLC-MS/MS; Paper modification; Psycho-neurological disorder toxin identification; Solid phase extraction; Validation

DOI:  https://doi.org/10.1016/j.foodchem.2025.145369
Bioanalysis. 2025 Jul 09. 1-17

Liquid chromatography-tandem mass spectrometry methods for clinical quantitation of antibiotics.

Xingrui He, Wenqian Zhang, Feifan Xie.

  The accurate quantification of antibiotics in biological matrices is pivotal for supporting individualized medication, optimizing antibiotics therapy and addressing the global crisis of antimicrobial resistance (AMR). LC-MS/MS has emerged as the gold standard for clinical antibiotic quantification, particularly valued for its accuracy, multiplexing efficiency, and compatibility with complex sample types. This review provides a comprehensive overview of the principles, methodologies, and clinical applications of LC-MS/MS in antibiotic quantification, with a focus on its role in therapeutic drug monitoring (TDM), pharmacokinetics (PK), and epidemiological studies. Key challenges, including sample preparation and matrix effects, are critically discussed. Tailored strategies for analyzing diverse antibiotic classes (e.g. β-lactams, aminoglycosides, colistins, macrolides, and glycopeptides) are highlighted by considering their physicochemical properties, including polarity, acid-base characteristics, and structural complexity. Furthermore, emerging trends in automation, high-resolution mass spectrometry, and quality control frameworks are outlined to guide future advancements. By bridging technological innovation with clinical needs, LC-MS/MS continues to be a cornerstone of precision medicine and a vital tool in global AMR mitigation efforts.

Keywords:  LC-MS/MS; antibiotics; antimicrobial resistance; pharmacokinetics; therapeutic drug monitoring

DOI:  https://doi.org/10.1080/17576180.2025.2529149
Rapid Commun Mass Spectrom. 2025 Oct 30. 39(20): e10104

Critical Method Parameters to Evaluate When Developing a Method Using a Laser Diode Thermal Desorption (LDTD) Coupled to a Mass Spectrometer.

Jonathan Rochon, Serge Auger, Eshwar Jagerdeo.

   RATIONALE: This paper presents an in-depth evaluation of the laser diode thermal desorption (LDTD) device interfaced to a mass spectrometer and identifies the critical method parameters to evaluate when developing a new procedure.
METHODS: Samples were solvent extracted and spotted in a 96-well plate. In the case of biological fluids, hydrolysis followed by solid phase extraction is required. The solvent in the 96-well plate is evaporated, followed by mass spectrometric analysis (MS) with atmospheric pressure chemical ionization (APCI). Where applicable, the instrument is operated in a data-dependent mode, with a full-scan mass spectrum followed by MS/MS spectra with a total runtime of 18 s per well.
RESULTS: Five key experiments (sample dilution, gas flow, laser ramp, ion saturation/ion suppression, and signal enhancement) were evaluated as critical parameters that could potentially be encountered in method development, and practical solutions are proposed.
CONCLUSIONS: Interfacing LDTD with a mass spectrometer allows for rapid screening for many analytes in a wide range of samples, with either minimal or complex sample preparation. Addressing all critical method parameters can aid in creating a sensitive and robust procedure.

Keywords:  LDTD; ambient ionization; laser diode thermal desorption; mass spectrometer; method development

DOI:  https://doi.org/10.1002/rcm.10104
J Am Soc Mass Spectrom. 2025 Jul 10.

Assessment of Variable Traveling Wave Profiles for Small-Molecule Applications in Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS).

James N Dodds, Amie M Solosky, Sadie M Disselkoen, Kara M Joseph, Erin S Baker.

The MOBILion MOBIE system is a relatively new platform offering high ion mobility spectrometry (IMS) resolving power and resolution. While these advancements present encouraging opportunities for isomer separations and improved molecular annotation, previous studies have noted that collision cross section (CCS) values collected on the MOBIE and other traveling wave (TW) systems possess bias in calculated CCS values that limits the functionality of translating CCS libraries across multiple IMS platforms. Though these challenges persist, MOBILion recently released a software update (EyeOn v.2.3) that provides the capability of utilizing variable traveling wave profiles, which modulate the applied TW amplitude and frequency over the duration of each IMS scan to provide optimal transmission, IMS resolution, and scan speed. In this work, 5 variable TW profiles are assessed alongside a legacy "static" method for application toward future small-molecule workflows, tested herein with 3 model systems: per- and polyfluoroalkyl substances (PFAS), bile acids, and oxylipins. Using 3 primary evaluation metrics, including (1) ion transmission, (2) IMS resolution of isomeric species, and (3) relative ease of CCS conversion and mobility filtering, the collective results illustrate that the "Full" TW profile possesses many advantages when analyzing small molecules for nontargeted applications. Although the bias in TW-based CCS measurements vs previous DTIMS values remains, utilizing CCS values obtained with a consistent variable TW profile enables a linear calibration procedure, which facilitates routine mobility filtering of IMS-MS data by CCS and represents a needed improvement for streamlining both data acquisition and subsequent analysis.

DOI: https://doi.org/10.1021/jasms.5c00140
J Chromatogr A. 2025 Jun 14. pii: S0021-9673(25)00496-0. [Epub ahead of print]1758 466150

Determination of per- and polyfluoroalkyl substances in tissue using QuEChERS extraction followed by novel enhanced matrix removal mixed-mode passthrough cleanup with LC-MS/MS detection.

Limian Zhao, Carrie Xu, Emily Parry, Matthew Giardina.

  A novel multiresidue method was developed and validated for the quantification of 40 per- and polyfluoroalkyl substances (PFAS) in fish, poultry and terrestrial animal muscle tissues. The method integrates QuEChERS extraction with an enhanced matrix removal (EMR) mixed-mode passthrough cleanup, followed by LC-MS/MS analysis. Validation was performed using tilapia, chicken, and pork matrices, assessing method suitability, selectivity, method detection limits (MDLs), limits of quantitation (LOQs), quantitation accuracy, intra- and inter- batch precision, internal standard recovery and repeatability (both extracted and non-extracted). The method was further cross-validated in cod, canned tuna, beef, and turkey, evaluating suitability and selectivity, MDLs, LOQ, and accuracy and precision at LOQ level. The new approach met all acceptance criteria outlined in EPA Method 1633 for tissue matrices, as well as the requirements of relevant EU regulations and AOAC SMPR guidelines. Target quantitation accuracy (apparent recovery) ranged from 72 - 151 % with over 95 % of analytes achieving accuracy within 80 - 120 % range. Precision, expressed as relative standard deviation (RSD), was below 20 % for all compounds across all tested tissue matrices. Internal standard recoveries, both extracted and non-extracted ranged, ranged from 57 to 202 %, with RSD below 9.4 %. Validated LOQs ranged from 0.05 - 1.25 ng/g, while calculated MDLs spanned 0.003 to 0.185 ng/g across the various tissue matrices. Compared to the conventional solvent extraction and solid phase extraction (SPE) approach outlined in EPA Method 1633, this method demonstrated enhanced accuracy, precision, and operational efficiency, resulting in significant time and cost savings.

Keywords:  EMR mixed-mode passthrough cleanup; EPA Method 1633; LC-MS/MS; Method development and validation; Per- and Polyfluoroalkyl Substances (PFAS); QuEChERS extraction; Tissue matrices

DOI:  https://doi.org/10.1016/j.chroma.2025.466150
J Sep Sci. 2025 Jul;48(7): e70210

A Supercritical Fluid Chromatographic Method for the Determination and Separation of Boronic Acids.

Upputuri Harikrishna, Punniyavel Jeyavel Pandiyan, Kaveesha Srinivas Suryakoppa, Ramesh Appadurai, Vivek Hamse Kameshwar, Shwetha Hosahalli Nanjundappa, Nandeesh Kebbahalli Nagalingaiah.

  A green and high-throughput chromatography method was developed for the separation and quantification of boronic acids using an environmentally friendly supercritical fluid chromatography (SFC). The developed method was successfully applied for the separation of a mixture of five boronic acid compounds having different functional groups and also used for the quantification of over 15 wide ranges of boronic acid and boronic ester compounds. Expanding this method, reaction monitoring studies were performed to analyze the boronic acids present in the organic reaction mixtures obtained from the Suzuki coupling reaction, Arylation of amine, and Arylation of phenol reactions. The mobile phase used for this analysis was supercritical carbon dioxide modified by 8%-40% of methanol, which contained 20 mM aqueous ammonia (25%) as an additive, and the stationary phase used was 2-ethylpyridine-bonded silica. Overall runtime of the optimized method was 7 min with back pressure of 100 bar at a column temperature of 40°C. An extensive study was performed to optimize the various method parameters, such as columns, mobile phase modifier, additives, back pressure, and temperature. The validated SFC method was found to give a relative standard deviation of interday and intraday peak average area precision of each compound (A-E). The precision of the analytical method was evaluated based on the %RSD of the peak areas for each compound under both intraday and interday conditions. Despite slight variations, all intraday %RSD values were well within the acceptable range of analytical precision (<2%). The LOD and LOQ were in the range from 0.02 to 20 µg/mL and from 0.2 to 100 µg/mL respectively, for the five boronic acids compounds studied.

Keywords:  2‐Ethylpyridine silica column; boronic acid; purification; supercritical fluid chromatography (SFC)

DOI:  https://doi.org/10.1002/jssc.70210
Sci Rep. 2025 Jul 08. 15(1): 24548

Method development for correlating lipid molecular information with anatomy in C. elegans.

Sara Mandic, Bryn Flinders, Michiel Vandenbosch, Akane Ohta, Atsushi Kuhara, Ron M A Heeren, Masazumi Fujiwara.

Caenorhabditis elegans (C. elegans) is an important model organism for studying fat storage and lipid metabolism. Mass-spectrometry imaging (MSI) is an emerging technology for mapping the spatial distribution of lipids. However, MSI analysis of C. elegans is limited by the lack of reproducible sample preparation methods. Here, we present a microfluidics-based workflow for preparing consecutive nematode sections while retaining their internal structures, such as the pharynx, intestine, and embryos. This method enables multimodal analysis of single nematodes by MSI and Oil Red O staining, revealing a number of lipids spatially distributed across different body parts. The feature-based image reconstruction technique enables the three-dimensional reconstruction of nematodes based on optical images and MSI-based lipid mapping. The present method can correlate MSI data with various imaging modalities to provide detailed correlations between anatomical features and lipid distribution in nematodes.

DOI: https://doi.org/10.1038/s41598-025-09577-9
Talanta. 2025 Jul 05. pii: S0039-9140(25)01046-X. [Epub ahead of print]297(Pt A): 128556

Quantitative quadrupolar NMR (qQNMR) determination of taurine in undiluted human urine samples using 1D and 2D 33S NMR.

Arantxa Forte-Castro, Ana Belén Ruiz-Muelle, Ignacio Fernández.

  A quantitative quadrupolar nuclear magnetic resonance (qQNMR) method based on sulfur-33 (33S) NMR has been developed for the direct, dilution-free determination of taurine in human urine, addressing matrix challenges in biofluid analysis. The 1D33S approach exhibited linearity (14-70 mg mL-1; R2 = 0.9993), LOD = 6.78 ± 0.66 mg mL-1, LOQ = 10.84 ± 0.69 mg mL-1, precision <1.1 % CV, and recoveries of 96.95-101.58 % with negligible matrix effect (-3.15 %). External calibration using ammonium sulfate yielded similar results. Critically, 2D 1H-33S gHMBC experiments reduced LOD/LOQ to 1.2/4.0 mg mL-1 by leveraging 1H sensitivity. The method enables rapid (<12 min), robust analysis without sample pretreatment, offering a practical alternative to chromatographic techniques for high-concentration urinary taurine quantification.

Keywords:  (33)S NMR; Quadrupolar nuclei; Taurine; Urine; qNMR

DOI:  https://doi.org/10.1016/j.talanta.2025.128556
Anal Bioanal Chem. 2025 Jul 09.

Liquid chromatography-mass spectrometry approach for characterizing sucrose isomers in complex mono-floral honey.

Enoch Amoah, Santosh Raman Acharya, Ayesha Seth, Abraham K Badu-Tawiah.

  Sucrose, which forms < 2% of the chemical content in honey samples, is known to have five structural isomers each with its own medicinal benefits. Unfortunately, studies characterizing the specific sucrose isomer(s) present in honey samples are limited. Herein, we introduce a contained electrospray ionization (cESI) method that can be coupled between liquid chromatography (LC) and tandem mass spectrometry (MS/MS). This LC-cESI-MS/MS platform leverages chloride adduction to enable sensitive differentiation and characterization of disaccharide isomers in complex honey samples. By integrating retention time and collision-induced dissociation (CID) MS/MS data, we achieved orthogonal analysis of six sucrose isomers. The MS/MS on the chloride adducts showed distinct fragment ions for each isomer. Additional optimization afforded nanomolar (nM) detection limits for all disaccharides analyzed via chloride adduction in negative-ion mode, a feature that showed superior sensitivity compared with conventional sodium adduction methods typically achieved in positive-ion mode. We identified four sucrose isomers (turanose, palatinose, maltulose, and trehalulose) in three mono-floral honey samples, of which turanose was the most abundant isomer. Sucrose itself could not be confirmed in any of the honey samples tested and leucrose was confirmed to be absent. Although the specific amounts of these isomers were not determined, principal component analysis showed that the abundances of the four identified structural isomers significantly differed in the three mono-floral honey samples. The current study forms the first report suggesting turanose to be the main sucrose isomer in the tested mono-floral honey. Such identification was made possible because of our ability to independently optimize LC and cESI spray solvents, and to enable online microdroplet chemistry via chloride adduction, which allowed the conventional CID-MS/MS to yield highly informative fragmentation.

Keywords:  Analytical methods; Liquid chromatography-mass spectrometry; Microdroplet chemistry; Mono-floral honey; Sucrose isomers

DOI:  https://doi.org/10.1007/s00216-025-05988-9
bioRxiv. 2025 Jul 05. pii: 2025.07.02.662857. [Epub ahead of print]

Transformer-based Deep Learning for Glycan Structure Inference from Tandem Mass Spectrometry.

Ejas Althaf Abtheen, Arun Singh, Shyam Sriram, Changyou Chen, Sriram Neelamegham, Rudiyanto Gunawan.

Glycans play critical roles in diverse biological processes, but their structural analysis by tandem mass spectrometry (MS/MS) remains a major challenge due to their branched structure and stereochemistry. Traditional computational methods, such as database searching, are constrained by the scope of existing libraries and can be computationally intensive. While recent deep learning models have advanced the field, they often struggle to capture the complex, long-range dependencies within MS/MS spectra required for accurate inference. To address these challenges, we present GlycoBERT and GlycoBART, novel transformer-based models for glycan structure prediction from MS/MS data. GlycoBERT, a sequence classifier, achieves 95.1% structural accuracy on test data, surpassing the current state-of-the-art deep learning model, CandyCrunch. However, classification-based methods are inherently limited to predicting structures present in the training data. To overcome this, we developed GlycoBART, a generative sequence-to-sequence model capable of de novo glycan inference. On independent validation datasets, both models demonstrate robust performance. Critically, when applied to an MS/MS dataset from human embryonic kidney cells, GlycoBART generated two de novo glycan structures absent from the training set, one of which is a novel structure not catalogued in major glycan databases. Together, GlycoBERT and GlycoBART establish a new benchmark for glycan analysis, offering a powerful framework that enables more accurate and comprehensive exploration of glycan diversity and discovery.

DOI: https://doi.org/10.1101/2025.07.02.662857
J Sep Sci. 2025 Jul;48(7): e70206

Rapid Screening of 25 Environmental Hormones in Aquatic Products Using QuEChERS-Combined With Dispersive Liquid-Liquid Microextraction Based on Solidification of Floating Organic Droplet Coupled With UHPLC-Q/Orbitrap HRMS.

Jiwang Tang, Yong Xiao, Hongqing Zhao, Can Li, Xiong Hu, Wenbin He.

  An innovative analytical method integrating QuEChERS with dispersive liquid-liquid microextraction using solidified floating organic droplets (DLLME-SFO) and ultra-high-performance liquid chromatography-quadrupole/orbitrap high-resolution mass spectrometry (UHPLC-Q/Orbitrap HRMS) was developed for the rapid screening of 25 environmental hormones (EHs) in aquatic products. The method systematically optimized key parameters, including extraction solvent selection (1-undecanol), water volume (5 mL), pH (native pH 6.5), adsorbent combination (C18/PSA, 20 mg each), and salt addition (0% NaCl), achieving high sensitivity with detection limits of 0.1-0.4 µg/kg and recoveries of 68.2%-112.8%. The method demonstrated excellent linearity (R2 > 0.995) across a concentration range of 0.4-40 µg/kg, with precision (intra- and inter-day RSDs < 15%) and manageable matrix effects (-19.5% to 10.9%). The environmental impact assessment, conducted using the Analytical GREEnness Metric for Sample Preparation (AGREEprep score: 0.59) and Blue Applicability Grade Index (BAGI score: 80), confirmed that the proposed method satisfies both sustainability and practicality criteria for EHs analysis. Enhanced matrix purification and dual-polarity HRMS detection enabled accurate identification and quantification of structurally diverse EHs, including pesticides and pharmaceuticals. Validated in 60 commercial samples, the method detected prometryn residues in 11.7% of cases, demonstrating its practicality for monitoring EH contamination in complex aquatic matrices. This approach represents a significant advancement in multi-residue analysis, combining efficiency, sensitivity, and environmental compatibility.

Keywords:  aquatic products; dispersive liquid–liquid microextraction; environmental endocrine disruptors; high‐resolution mass spectrometry; multi‐residue screening

DOI:  https://doi.org/10.1002/jssc.70206
J Mass Spectrom. 2025 Aug;60(8): e5157

The Future of a Myriad of Accelerated Biodiscoveries Lies in AI-Powered Mass Spectrometry and Multiomics Integration.

Aivett Bilbao.

The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS-based "omics" research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains, from health to environment and industrial biotechnology. Beginning with an overview of key challenges inherent in MS software pipelines, this personal perspective explores how AI-driven solutions can address them to enhance data processing, integration and interpretation. It proposes a paradigm shift in molecular identification and quantitation algorithms, leveraging AI to enable holistic interpretation of MS-based multiomics data. While centered on MS-based omics, this holistic AI-driven paradigm is also critical for connecting dynamic biochemical changes to genomics and transcriptomics contexts, reinforcing the integrative value of MS in multiomics research. Ultimately, this AI-driven approach could enhance efficiency, accuracy, and molecular breadth of coverage, deepening our systems-level understanding of biological processes and accelerating a myriad of biodiscoveries.

DOI: https://doi.org/10.1002/jms.5157
Nat Commun. 2025 Jul 10. 16(1): 6398

Orbitrap noise structure and method for noise unbiased multivariate analysis.

Michael R Keenan, Gustavo F Trindade, Alexander Pirkl, Clare L Newell, Yuhong Jin, Konstantin Aizikov, Andreas Dannhorn, Junting Zhang, Lidija Matjačić, Henrik Arlinghaus, Anya Eyres, Rasmus Havelund, Richard J A Goodwin, Zoltan Takats, Josephine Bunch, Alex P Gould, Alexander Makarov, Ian S Gilmore.

Orbitrap mass spectrometry is widely used in the life-sciences. However, like all mass spectrometers, non-uniform (heteroscedastic) noise introduces bias in multivariate analysis complicating data interpretation. Here, we study the noise structure of an Orbitrap mass analyser integrated into a secondary ion mass spectrometer (OrbiSIMS). Using a stable primary ion beam to provide a well-controlled source of ions from a silver sample, we find that noise has three characteristic regimes: at low signals the Orbitrap detector noise and a censoring algorithm dominates; at intermediate signals counting noise specific to the ion emission process is most significant; and at high signals additional sources of measurement variation become important. Using this understanding, we developed a generative model for Orbitrap data that accounts for the noise distribution and introduce a scaling method, termed WSoR, to reduce the effects of noise bias in multivariate analysis. We compare WSoR performance with no-scaling and existing scaling methods for three biological imaging data sets including drosophila central nervous system, mouse testis and a desorption electrospray ionisation (DESI) image of a rat liver. WSoR consistently performed best at discriminating chemical information from noise. The performance of the other methods varied on a case-by-case basis, complicating the analysis.

DOI: https://doi.org/10.1038/s41467-025-61542-2
J Chromatogr A. 2025 Jul 01. pii: S0021-9673(25)00533-3. [Epub ahead of print]1758 466187

Simultaneous analysis of organic and inorganic explosive traces by online two-dimensional liquid chromatography.

Rick S van den Hurk, Ekaterina Belina, Joshka Verduin, Sofie Lazeroms, Pascal Camoiras González, Robert C Huls, Ron A H Peters, Annemieke W C Hulsbergen, Arian C van Asten, Bob W J Pirok.

  To investigate and process a crime scene after an explosion, analytical methods that can detect trace amounts of explosive material are essential. These chemical traces are of high chemical diversity, encompassing both inorganic and organic materials of forensic interest requiring different analytical techniques for characterization. In this work, we developed a workflow that allows for, the simultaneous separation and detection of inorganic anions, cations, and organic explosive materials from a single injection. A heart-cutting two-dimensional liquid chromatography (2D-LC) method was developed. In the first dimension, hydrophilic interaction chromatography (HILIC) was applied for the separation of inorganic anions and cations. The use of active solvent modulation enabled transfer and refocusing of the organic fraction to a reversed-phase LC (RPLC) separation. The detection of ammonium was challenging using this analysis strategy. To enable sensitive detection of ammonium, a derivatization protocol was developed. The mobile phases of both separation dimensions are compatible with mass spectrometry, allowing for even more sensitive detection and selective, admissible identification. In this work, a combination of evaporative light scattering and ultraviolet absorption was used for detection of all the analytes. The developed HILIC - RPLC method was capable of analyzing different classes of explosives using a single method, reducing the required sample amounts and analysis time, thereby potentially enabling a faster, more efficient, and less work-intensive handling of explosive-related casework in forensic laboratories.

Keywords:  Active solvent modulation; Energetic materials; Explosives trace analysis; HILIC-RPLC; Heart-cut 2D-LC

DOI:  https://doi.org/10.1016/j.chroma.2025.466187