bims-metlip 2024-04-07 papers

bims-metlip

Biomed News

on Methods and protocols in metabolomics and lipidomics

Issue of 2024–04–07
twenty-one papers selected by
Sofia Costa, Matterworks

High-Throughput Acoustic Ejection Mass Spectrometry with Adjustable Signal Durations.
Comprehensive Metabolomic Analysis of Human Heart Tissue Enabled by Parallel Metabolite Extraction and High-Resolution Mass Spectrometry.
Rapid determination of glyphosate and glufosinate in human blood by probe electrospray ionization tandem mass spectrometry.
Development, validation, and clinical application of a UPLC-MS/MS method for omadacycline determination in human serum.
Handling of problematic ion chromatograms with the Automated Target Screening (ATS) workflow for unsupervised analysis of high-resolution mass spectrometry data.
A UPLC-MS/MS method for simultaneous determination of arachidonic acid, stearic acid, and related endocannabinoids in human plasma.
Multinozzle Emitter for Improved Negative Mode Analysis of Reduced Native N-Glycans by Microflow Porous Graphitized Carbon Liquid Chromatography Mass Spectrometry.
Impact of Extraction Methods and Transportation Conditions on Lipid Profiles of Bovine Oocytes.
Tailored Mass Spectral Data Exploration Using the SpecXplore Interactive Dashboard.
Therapeutic Drug Monitoring of 6 New-Generation Antiseizure Medications Using a Mass Spectrometry Method: Analysis of 2-Year Experience in a Large Cohort of Korean Epilepsy Patients.
Shotgun Lipidomic Profiling of Sebum Lipids via Photocatalyzed Paternò-Büchi Reaction and Ion Mobility-Mass Spectrometry.
LC-MS/MS method for quick detection of vonoprazan fumarate in human plasma: Development, validation and its application to a bioequivalence study.
Energy Resolved Mass Spectrometry for Interoperable Non-resonant Collisional Spectra in Metabolomics.
Optimization, validation, and application of a liquid chromatography-tandem mass spectrometry method for the determination of 47 banned drug and related chemical residues in livestock urine using graphitized carboxyl multi-walled carbon nanotubes-based QuEChERS extraction.
Comprehensive Lipidomic Automation Workflow using Large Language Models.
Profiling Intact Glycosphingolipids with Automated Structural Annotation and Quantitation from Human Samples with Nanoflow Liquid Chromatography Mass Spectrometry.
Development of an LC-MS/MS method for the determination of five psychoactive drugs in postmortem urine by optimization of enzymatic hydrolysis of glucuronide conjugates.
[Determination of adenosine content in heart tissue by ultra performance liquid chromatography-triple quadrupole mass spectrometry].
Simultaneous determination of folic acid photolysis products and oxidized guanine derivatives in plasma by liquid chromatography-tandem mass spectrometry.
The IDSM mass spectrometry extension: searching mass spectra using SPARQL.
In-silico method development and optimization of on-line comprehensive two-dimensional liquid chromatography via a shortcut model.

Anal Chem. 2024 Mar 30.

High-Throughput Acoustic Ejection Mass Spectrometry with Adjustable Signal Durations.

Jing Ma, Chiu Cheong Aw, Heguang Ji, Shuxian Lin, Xuejiao Yin, Huiyin Tey, Chang Liu.

High-throughput mass spectrometry (MS) has witnessed rapid advancements and has found extensive applications across various disciplines. It enables the fast and accurate analysis of large sample sets, delivering a 10-fold or greater enhancement in analytical throughput when compared to conventional LC-MS methods. However, the signal duration in these high-throughput MS technologies is typically confined to a narrow range, presenting challenges for workflows demanding prolonged signal durations. In this study, we introduce a method that enables precise modulation of the signal duration on an acoustic ejection mass spectrometry (AEMS) system while ensuring high signal reproducibility. This flexibility allows for simultaneous and precise analysis of a significantly greater number of MS/MS transitions in high-throughput MS environments. Additionally, it offers a unique approach for parameter optimization and method development with minimal sample volume requirements. This advancement enhances the efficiency of MS-based analyses across diverse applications and facilitates broader utilization of MS technologies in high-throughput settings, including data-dependent acquisition (DDA) and data-independent acquisition (DIA).

DOI: https://doi.org/10.1021/acs.analchem.3c05167
Anal Chem. 2024 Apr 03.

Comprehensive Metabolomic Analysis of Human Heart Tissue Enabled by Parallel Metabolite Extraction and High-Resolution Mass Spectrometry.

Benjamin Wancewicz, Melissa R Pergande, Yanlong Zhu, Zhan Gao, Zhuoxin Shi, Kylie Plouff, Ying Ge.

The heart contracts incessantly and requires a constant supply of energy, utilizing numerous metabolic substrates, such as fatty acids, carbohydrates, lipids, and amino acids, to supply its high energy demands. Therefore, a comprehensive analysis of various metabolites is urgently needed for understanding cardiac metabolism; however, complete metabolome analyses remain challenging due to the broad range of metabolite polarities, which makes extraction and detection difficult. Herein, we implemented parallel metabolite extractions and high-resolution mass spectrometry (MS)-based methods to obtain a comprehensive analysis of the human heart metabolome. To capture the diverse range of metabolite polarities, we first performed six parallel liquid-liquid extractions (three monophasic, two biphasic, and one triphasic) of healthy human donor heart tissue. Next, we utilized two complementary MS platforms for metabolite detection: direct-infusion ultrahigh-resolution Fourier-transform ion cyclotron resonance (DI-FTICR) and high-resolution liquid chromatography quadrupole time-of-flight tandem MS (LC-Q-TOF-MS/MS). Using DI-FTICR MS, 9644 metabolic features were detected where 7156 were assigned a molecular formula and 1107 were annotated by accurate mass assignment. Using LC-Q-TOF-MS/MS, 21,428 metabolic features were detected where 285 metabolites were identified based on fragmentation matching against publicly available libraries. Collectively, 1340 heart metabolites were identified in this study, which span a wide range of polarities including polar (benzenoids, carbohydrates, and nucleosides) as well as nonpolar (phosphatidylcholines, acylcarnitines, and fatty acids) compounds. The results from this study will provide critical knowledge regarding the selection of appropriate extraction and MS detection methods for the analysis of the diverse classes of human heart metabolites.

DOI: https://doi.org/10.1021/acs.analchem.3c04353
J Chromatogr A. 2024 Mar 27. pii: S0021-9673(24)00220-6. [Epub ahead of print]1722 464846

Rapid determination of glyphosate and glufosinate in human blood by probe electrospray ionization tandem mass spectrometry.

Jiahua Ji, Yunfeng Zhang, Bo Zou, Linpei Dong, Aihua Wang, Xiaojun Wu, Hong Zhou, Zhenhe Chen, Ying Zhang, Yao Liu.

  In forensic science, glyphosate (GLYP) and glufosinate (GLUF), a class of non-selective broad-spectrum herbicides, have been frequently encountered in many fatal poisoning and suicide cases due to their widespread availability. Therefore, it is essential to develop an effective method for detecting these compounds. Some conventional methods, such as gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS), have been reported to detect these compounds. However, these methods are not ideal for their time-consuming and non-sensitive feature. Herein, probe electrospray ionization (PESI) tandem mass spectrometry (MS/MS), a fast and sensitive technique, was applied for the determination of GLYP and GLUF in human blood, which can obtain analytical results within 0.5 min without derivatization and chromatographic separation. After protein precipitation of blood samples, the supernatant was mixed with isopropanol and ultra-pure water (1:1 v/v). Then, 8 μL of the mixture was introduced into the plastic sample plate for PESI-MS/MS analysis. The limits of detection (LODs) of the method were 0.50 μg/mL and 0.25 μg/mL for two analytes, and the limits of quantitation (LOQs) were both 1.00 μg/mL, which are higher than the concentration of reported poisoning and fatal cases. In the linear range of 1-500 μg/mL, the regression coefficients (r2) for GLYP and GLUF were over 0.99. The matrix effects ranged from 94.8 % to 119.5 %, and the biases were below 4.3 %. The recoveries ranged between 84.8 % and 107.4 %, and the biases were below 7.6 %. Meanwhile, the method was effectively utilized to detect and quantify the blood, urine, and other samples. Consequently, the results suggest that PESI-MS/MS is a straightforward, fast, and sensitive method for detecting GLUF and GLYP in forensics. In the future, PESI-MS/MS will become an indispensable technique for polar substances in grassroots units of public security where rapid detection is essential.

Keywords:  Blood; Glufosinate; Glyphosate; Probe electrospray ionization; Tandem mass spectrometry

DOI:  https://doi.org/10.1016/j.chroma.2024.464846
J Pharmacol Toxicol Methods. 2024 Apr 02. pii: S1056-8719(24)00013-3. [Epub ahead of print] 107503

Development, validation, and clinical application of a UPLC-MS/MS method for omadacycline determination in human serum.

Guo Suhang, Zheng Ren, Fan Xudong, Zhang Ruoying, Cai Xinjun, Jin Jie.

   BACKGROUND: Omadacycline is the first aminomethyl-tetracycline variety to successfully enter clinical applications. To support regular therapeutic drug monitoring (TDM) in clinical practice, an ultra-high-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) method was developed that would allow omadacycline quantification in human serum.
METHODS: Proteins were precipitated from serum samples using methanol. Tigecycline was used as the internal standard. Mobile phase A was formic acid in water (0.1% v/v) and mobile phase B was methanol. UPLC-MS/MS was performed for analyte separation using a gradient elution program at a flow rate of 0.3 mL/min and a total run time of 5 min. The chromatography column was a ZORBAX PRHD SB-Aq (3 × 50 mm, 1.8 μm, Agilent, USA). The multiple reaction monitoring transitions at m/z = 557.4/470.3 and 586.5/513.3 were selected for omadacycline and tigecycline in the positive mode, respectively.
RESULTS: The validated curve ranges were 0.5-25.0 μg/mL. This method exhibited acceptable selectivity, matrix effects, and recovery. The inter- and intra-run accuracies ranged from 93.5% to 114.8%, and the inter- and intra-run precisions were between 1.29% and 5.55%.
CONCLUSIONS: The LC-MS/MS method provided a simple, specific, and rapid quantification of omadacycline in the serum of patients with pulmonary infection.

Keywords:  LC-MS/MS; Omadacycline; Therapeutic drug monitoring

DOI:  https://doi.org/10.1016/j.vascn.2024.107503
Anal Bioanal Chem. 2024 Apr 01.

Handling of problematic ion chromatograms with the Automated Target Screening (ATS) workflow for unsupervised analysis of high-resolution mass spectrometry data.

Georg Braun, Martin Krauss, Stephanie Spahr, Beate I Escher.

  Liquid chromatography (LC) or gas chromatography (GC) coupled to high-resolution mass spectrometry (HRMS) is a versatile analytical method for the analysis of thousands of chemical pollutants that can be found in environmental and biological samples. While the tools for handling such complex datasets have improved, there are still no fully automated workflows for targeted screening analysis. Here we present an R-based workflow that is able to cope with challenging data like noisy ion chromatograms, retention time shifts, and multiple peak patterns. The workflow can be applied to batches of HRMS data recorded after GC with electron ionization (GC-EI) and LC coupled to electrospray ionization in both negative and positive mode (LC-ESIneg/LC-ESIpos) to perform peak annotation and quantitation fully unsupervised. We used Orbitrap HRMS data of surface water extracts to compare the Automated Target Screening (ATS) workflow with data evaluations performed with the vendor software TraceFinder and the established semi-automated analysis workflow in the MZmine software. The ATS approach increased the overall evaluation performance of the peak annotation compared to the established MZmine module without the need for any post-hoc corrections. The overall accuracy increased from 0.80 to 0.86 (LC-ESIpos), from 0.77 to 0.83 (LC-ESIneg), and from 0.67 to 0.76 (GC-EI). The mean average percentage errors for quantification of ATS were around 30% compared to the manual quantification with TraceFinder. The ATS workflow enables time-efficient analysis of GC- and LC-HRMS data and accelerates and improves the applicability of target screening in studies with a large number of analytes and sample sizes without the need for manual intervention.

Keywords:  Automation; MZmine; Mass spectrometry; Target screening; TraceFinder; Workflow

DOI:  https://doi.org/10.1007/s00216-024-05245-5
Heliyon. 2024 Apr 15. 10(7): e28467

A UPLC-MS/MS method for simultaneous determination of arachidonic acid, stearic acid, and related endocannabinoids in human plasma.

Xiaojing Qian, Wangzhenzu Liu, Ying Chen, Jiaqi Zhang, Yuanye Jiang, Lingyun Pan, Cheng Hu.

  Endocannabinoids (eCBs) exert considerable influence over energy metabolism, lipid metabolism, and glucose metabolism within the human body. Among the most biologically active cannabinoids identified thus far are 2-arachidonoylglycerol (2-AG), arachidonoyl ethanolamide (AEA), 1-stearoylglycerol (1-SRG), and stearoyl ethanolamide (SEA), which are derived from arachidonic acid (AA) and stearic acid (SA). However, despite the unique in bioactivities exhibited by eCBs, their determination in plasma has been hindered by the lack of sensitive analytical methods. The aim of this study was to develop and validate a highly sensitive and rapid method using ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) for accurate measurement of AEA, SEA, 2-AG, 1-SRG, AA, and SA levels in human plasma samples. Sample preparation involved a protein precipitation method and a methyl tert-butyl ether liquid-liquid extraction method. Chromatographic separation was accomplished by utilizing an ACQUITY UPLC BEH C8 column with a mobile phase of acetonitrile containing 0.1% formic acid and water containing 0.1% formic acid, flowing at a rate of 0.35 mL/min. AA-d8, 2-AG-d5, and AEA-d8 were selected as deuterated internal standards. The analytes were determined with MRM in both positive and negative ion mode. The lower limit of quantification ranged from 0.1 to 400 ng/mL, and the correlation coefficient (R2) was >0.99. Inter-day and intra-day precision exhibited values of 0.55-13.29% and 0.62%-13.90%, respectively. Recovery and matrix effect were within the range of 77.7%-109.7%, and 90.0%-113.5%, respectively. Stability tests confirmed the acceptability of all analytes. To demonstrate the effectiveness of the approach, it was implemented to assess and compare plasma samples from healthy volunteers (n = 49) and individuals with non-alcoholic fatty liver disease (NAFLD) (n = 62). The study revealed significant differences in AEA, SEA, AA, and SA levels between the two groups.

Keywords:  Arachidonic acid; Endocannabinoids; LC-MS/MS; NAFLD; Stearic acid

DOI:  https://doi.org/10.1016/j.heliyon.2024.e28467
Anal Chem. 2024 Apr 01.

Multinozzle Emitter for Improved Negative Mode Analysis of Reduced Native N-Glycans by Microflow Porous Graphitized Carbon Liquid Chromatography Mass Spectrometry.

Melinda Wojtkiewicz, Sabarinath Peruvemba Subramanian, Rebekah L Gundry.

Microflow porous graphitized carbon liquid chromatography (PGC-LC) combined with negative mode ionization mass spectrometry (MS) provides high resolution separation and identification of reduced native N-glycan structural isomers. However, insufficient spray quality and low ionization efficiency of N-glycans present challenges for negative mode electrospray. Here, we evaluated the performance of a recently developed multinozzle electrospray source (MnESI) and accompanying M3 emitter for microflow PGC-LC-MS analysis of N-glycans in negative mode. In comparison to a standard electrospray ionization source, the MnESI with an M3 emitter improves signal intensity, identification, quantification, and resolution of structural isomers to accommodate low-input samples.

DOI: https://doi.org/10.1021/acs.analchem.3c03649
Reprod Sci. 2024 Apr 01.

Impact of Extraction Methods and Transportation Conditions on Lipid Profiles of Bovine Oocytes.

Camila Bruna de Lima, Marcella Pecora Milazzotto, Alessandra Aparecida Vireque, Daniel Carlino Joaquim, Tiago Jose Paschoal Sobreira, Christina Ramires Ferreira.

  Lipids play numerous pivotal physiological roles in mammalian reproduction, being indispensable for oocyte competence acquisition and post-fertilization embryonic development. Profiling lipids in minute samples, such as oocytes, presents challenges but has been accomplished through mass spectrometry technologies like Multiple Reaction Monitoring (MRM) profiling. With the dual objectives of simplifying workflow and examining the influence of preanalytical conditions, we assessed whether transportation at room temperature affects the lipid profile of bovine oocytes. To this end, samples were prepared using either monophasic (methanol only) or biphasic liquid extraction protocols (Bligh & Dyer method) and transported either on dry ice or at room temperature inside sealed-vacuum packages to prevent lipid oxidation. Subsequently, employing a comprehensive method, we screened a list of 316 MRMs from 10 different lipid subclasses in oocyte lipid extracts. Principal Component Analysis (PCA) revealed similar lipid profiles concerning temperature during transportation, whereas clear differentiation among samples was observed based on the lipid extraction method. Univariate analysis indicated that the one-phase methanol extraction resulted in higher relative abundances of phospholipids, except for phosphatidylserines. Conversely, the Bligh & Dyer extraction favored the detection of neutral intracellular lipids (triacylglycerols, free fatty acids, cholesteryl esters, and acyl-carnitines). Consequently, lipid recovery was directly correlated with the polarity of lipid class and the extraction method. Regarding transportation temperature, phosphatidylethanolamine, triacylglycerol, and free fatty acids exhibited lower abundances when samples were transported at room temperature. Based on multivariate and univariate analyses, we conclude that if samples undergo the same lipid extraction protocol and are transported in the same batch at room temperature inside vacuum-sealed bags, it is feasible to analyze lipid extracts of bovine oocytes and still obtain informative lipid profiling results.

Keywords:  Bovine; Lipid extraction; Multiple Reaction Monitoring; Oocytes; Room temperature; Vacuum pressure

DOI:  https://doi.org/10.1007/s43032-024-01524-9
Anal Chem. 2024 Apr 02.

Tailored Mass Spectral Data Exploration Using the SpecXplore Interactive Dashboard.

Kevin Mildau, Henry Ehlers, Ian Oesterle, Manuel Pristner, Benedikt Warth, Maria Doppler, Christoph Bueschl, Jürgen Zanghellini, Justin J J van der Hooft.

Untargeted metabolomics promises comprehensive characterization of small molecules in biological samples. However, the field is hampered by low annotation rates and abstract spectral data. Despite recent advances in computational metabolomics, manual annotations and manual confirmation of in-silico annotations remain important in the field. Here, exploratory data analysis methods for mass spectral data provide overviews, prioritization, and structural hypothesis starting points to researchers facing large quantities of spectral data. In this research, we propose a fluid means of dealing with mass spectral data using specXplore, an interactive Python dashboard providing interactive and complementary visualizations facilitating mass spectral similarity matrix exploration. Specifically, specXplore provides a two-dimensional t-distributed stochastic neighbor embedding embedding as a jumping board for local connectivity exploration using complementary interactive visualizations in the form of partial network drawings, similarity heatmaps, and fragmentation overview maps. SpecXplore makes use of state-of-the-art ms2deepscore pairwise spectral similarities as a quantitative backbone while allowing fast changes of threshold and connectivity limitation settings, providing flexibility in adjusting settings to suit the localized node environment being explored. We believe that specXplore can become an integral part of mass spectral data exploration efforts and assist users in the generation of structural hypotheses for compounds of interest.

DOI: https://doi.org/10.1021/acs.analchem.3c04444
Arch Pathol Lab Med. 2024 Apr 05.

Therapeutic Drug Monitoring of 6 New-Generation Antiseizure Medications Using a Mass Spectrometry Method: Analysis of 2-Year Experience in a Large Cohort of Korean Epilepsy Patients.

Sang-Mi Kim, Won Young Heo, Hyeonju Oh, Eun Yeon Joo, Young-Min Shon, Seung Bong Hong, Soo-Youn Lee, Dae-Won Seo.

CONTEXT.—: New-generation antiseizure medications (ASMs) are increasingly prescribed, and therapeutic drug monitoring (TDM) has been proposed to improve clinical outcome. However, clinical TDM data on new-generation ASMs are scarce.
OBJECTIVE.—: To develop and validate a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for therapeutic drug monitoring (TDM) of 6 new-generation ASMs in serum and analyze the clinical TDM data from a large cohort of Korean patients with epilepsy.
DESIGN.—: Stable isotope-labeled internal standards were added to protein precipitations of serum. One microliter of sample was separated on Agilent Poroshell EC-C18 column, and lacosamide, perampanel, gabapentin, pregabalin, vigabatrin, and rufinamide were simultaneously quantified by Agilent 6460 triple-quad mass spectrometer in multiple-reaction monitoring mode. Linearity, sensitivity, precision, accuracy, specificity, carryover, extraction recovery, and matrix effect were evaluated. TDM data of 458 samples from 363 Korean epilepsy patients were analyzed.
RESULTS.—: The method was linear with limit of detection less than 0.05 μg/mL in all analytes. Intraassay and interassay imprecisions were less than 5% coefficient of variation. Accuracy was within ±15% bias. Extraction recovery ranged from 85.9% to 98.8%. A total of 88% (403 of 458) were on polypharmacy, with 29% (118 of 403) using concomitant enzyme inducers. Only 38% (175 of 458) of the concentrations were therapeutic, with 53% (244 of 458) being subtherapeutic. Drug concentration and concentration-to-dose ratio were highly variable among individuals in all 6 ASMs.
CONCLUSIONS.—: A simple and rapid LC-MS/MS method for TDM of 6 ASMs was developed and successfully applied to clinical practice. This large-scale TDM data could help establish an effective monitoring strategy for these drugs.

DOI: https://doi.org/10.5858/arpa.2023-0386-OA
Anal Chem. 2024 Mar 31.

Shotgun Lipidomic Profiling of Sebum Lipids via Photocatalyzed Paternò-Büchi Reaction and Ion Mobility-Mass Spectrometry.

Hengxue Shi, Yu Xia.

Sebum lipids are composed of nonpolar lipids, and they pose challenges for mass spectrometry-based analysis due to low ionization efficiency and the existence of numerous isomers and isobars. To address these challenges, we have developed ethyl 2-oxo-2-(pyridine-3-yacetate as a charge-tagging Paternò-Büchi reagent and Michler's ketone as a highly efficient photocatalyst, achieving ∼90% conversion for C═C derivatization under 440 nm LED irradiation. This derivatization, when coupled with electrospray ionization-tandem mass spectrometry, boosts the detection of sebum lipids and pinpoints C═C location in a chain-specific fashion. Identification and quantitation of isomers are readily achieved for wax esters, a class of underexplored sebum lipids, which have C═C bonds distributed in fatty alcohol and fatty acyl chains. A shotgun analysis workflow has been developed by pairing the offline PB derivatization with cyclic ion mobility spectrometry-mass spectrometry. Besides the dominant n-10 C═C location in unsaturated wax esters, profiling of low abundance isomers, including the rarely reported n-7 and n-13 locations, is greatly enhanced due to separations of C═C diagnostic ions by ion mobility. Over 900 distinct lipid structures from human sebum lipid extract have been profiled at the chain-specific C═C level, including wax esters (500), glycerolipids (393), and cholesterol esters (22), far more exceeding previous reports. Overall, we have developed a fast and comprehensive lipidomic profiling tool for sebum samples, a type of noninvasive biofluids holding potential for the discovery of disease markers in distal organs.

DOI: https://doi.org/10.1021/acs.analchem.4c00141
Biomed Chromatogr. 2024 Apr 01. e5860

LC-MS/MS method for quick detection of vonoprazan fumarate in human plasma: Development, validation and its application to a bioequivalence study.

Xinyan Chen, Tao Chen, Yunzhe Huang, Minhui Wang, Yaqin Wang, Ping Wu, Xiaocui Xia, Pengfei Du, Jianbang Wu, Jie Shen, Yuanwei Jia.

  A liquid chromatography-tandem mass spectrometry method with vonoprazan fumarate-d4 as a stable isotope-labeled internal standard was developed and validated aiming at quantification of vonoprazan fumarate in human plasma for a bioequivalence study. Chromatographic separation was achieved by acetonitrile one-step protein precipitation using a gradient elution of 0.1% formic acid aqueous solution and acetonitrile with a run time of 3.65 min. Detection was carried out on a tandem mass spectrometer in multiple reaction monitoring mode via a positive electrospray ionization interface. The multiple reaction monitoring mode of precursor-product ion transitions for vonoprazan fumarate and vonoprazan fumarate-d4 were m/z 346.0 → 315.1 and 350.0 → 316.0, respectively. The linear range was 0.150-60.000 ng/ml. This method was fully validated with acceptable results in terms of selectivity, carryover, lower limit of quantification, calibration curve, accuracy, precision, dilution effect, matrix effect, stability, recovery and incurred sample reanalysis. A successful application of this method was realized in the bioequivalence study of vonoprazan fumarate tablet (20 mg) among healthy Chinese volunteers.

Keywords:  LC–MS/MS; bioequivalence study; human plasma; vonoprazan fumarate

DOI:  https://doi.org/10.1002/bmc.5860
J Am Soc Mass Spectrom. 2024 Apr 01.

Energy Resolved Mass Spectrometry for Interoperable Non-resonant Collisional Spectra in Metabolomics.

Amandine Hueber, Hanna Kulyk, Annelaure Damont, Edith Nicol, Sandra Alves, Sophie Liuu, Martin Green, Justine Bertrand-Michel, Nicolas Cenac, François Fenaille, Jean-Claude Tabet.

In untargeted metabolomics, the unambiguous identification of metabolites remains a major challenge. This requires high-quality spectral libraries for reliable metabolite identification, which is essential for translating metabolomics data into meaningful biological information. Several attempts have been made to generate reproducible product ion spectra (PIS) under a low collision energy (ELab) regime and nonresonant collisional conditions but have not fully succeeded. We examined the ERMS (energy-resolved mass spectrometry) breakdown curves of two lipo-amino acids and showed the possibility to highlight "singular points", called descriptors hereafter (linked to respective ELab depending on the instrument), for each of the monomodal product ion profiles. Using several instruments based on different technologies, the PIS recorded at these specific ELab sites shows remarkable similarities. The descriptors appeared as being independent of the fragmentation mechanisms and can be used to overcome the main instrumental effects that limit the interoperability of spectral libraries. This proof-of-concept study, performed on two particular lipo-amino acids, demonstrates the high potential of ERMS-derived information to determine the instrument-specific ELab at which PIS recorded in nonresonant conditions become highly similar and instrument-independent, thus comparable across platforms. This innovative but straightforward approach could help remove some of the obstacles to metabolite identification in nontargeted metabolomics, putting an end to a challenging chimera.

DOI: https://doi.org/10.1021/jasms.3c00410
J Chromatogr A. 2024 Mar 30. pii: S0021-9673(24)00232-2. [Epub ahead of print]1721 464858

Optimization, validation, and application of a liquid chromatography-tandem mass spectrometry method for the determination of 47 banned drug and related chemical residues in livestock urine using graphitized carboxyl multi-walled carbon nanotubes-based QuEChERS extraction.

Youzhi Su, Jianjiang Lu, Jun Liu, Ning Wang, Fang Li, Hongqin Lei.

  The establishment of an efficient method for the analysis of drug residues in animal urine facilitates the real-time monitoring of drugs used in the production of animal-derived food. A modified QuEChERS extraction-liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was established for the determination of 47 banned drug and related chemical residues in livestock urine. The sample was extracted with acetonitrile by converting the acid-base environment. The sample cleanup effects of seven solid phase extraction cartridges and two EMR-Lipid products were compared, and three materials, including graphitized carboxyl multi-walled carbon nanotubes (MWCNTs), PSA, and C18, were selected as QuEChERS adsorbents from 24 materials. All analytes showed good linearity, with correlation coefficients (R2) greater than 0.9936. Low limits of quantification could be obtained, ranging from 0.2 to 5.5 ng/mL. The average recoveries at low, medium, and high spiked levels were in the range of 70.8-114.9 %, with intra-day precision ranging from 2.4 % to 11.2 % and inter-day precision ranging from 4.5 % to 16.1 %. Swine urine and bovine urine samples collected from different farms were effectively analyzed using the developed method, and metronidazole was detected in three swine urine samples.

Keywords:  Banned drugs; Graphitized carboxyl MWCNTs; LC–MS/MS; Livestock urine; QuEChERS

DOI:  https://doi.org/10.1016/j.chroma.2024.464858
ArXiv. 2024 Mar 22. pii: arXiv:2403.15076v1. [Epub ahead of print]

Comprehensive Lipidomic Automation Workflow using Large Language Models.

Connor Beveridge, Sanjay Iyer, Caitlin E Randolph, Matthew Muhoberac, Palak Manchanda, Amy C Clingenpeel, Shane Tichy, Gaurav Chopra.

Lipidomics generates large data that makes manual annotation and interpretation challenging. Lipid chemical and structural diversity with structural isomers further complicates annotation. Although, several commercial and open-source software for targeted lipid identification exists, it lacks automated method generation workflows and integration with statistical and bioinformatics tools. We have developed the Comprehensive Lipidomic Automated Workflow (CLAW) platform with integrated workflow for parsing, detailed statistical analysis and lipid annotations based on custom multiple reaction monitoring (MRM) precursor and product ion pair transitions. CLAW contains several modules including identification of carbon-carbon double bond position(s) in unsaturated lipids when combined with ozone electrospray ionization (OzESI)-MRM methodology. To demonstrate the utility of the automated workflow in CLAW, large-scale lipidomics data was collected with traditional and OzESI-MRM profiling on biological and non-biological samples. Specifically, a total of 1497 transitions organized into 10 MRM-based mass spectrometry methods were used to profile lipid droplets isolated from different brain regions of 18-24 month-old Alzheimer's disease mice and age-matched wild-type controls. Additionally, triacyclglycerols (TGs) profiles with carbon-carbon double bond specificity were generated from canola oil samples using OzESI-MRM profiling. We also developed an integrated language user interface with large language models using artificially intelligent (AI) agents that permits users to interact with the CLAW platform using a chatbot terminal to perform statistical and bioinformatic analyses. We envision CLAW pipeline to be used in high-throughput lipid structural identification tasks aiding users to generate automated lipidomics workflows ranging from data acquisition to AI agent-based bioinformatic analysis.
Anal Chem. 2024 Apr 02.

Profiling Intact Glycosphingolipids with Automated Structural Annotation and Quantitation from Human Samples with Nanoflow Liquid Chromatography Mass Spectrometry.

Ryan L Schindler, Armin Oloumi, Jennyfer Tena, Michael Russelle S Alvarez, Yiyun Liu, Sheryl Grijaldo, Mariana Barboza, Lee-Way Jin, Angela M Zivkovic, Carlito B Lebrilla.

Sphingolipids are an essential subset of bioactive lipids found in most eukaryotic cells that contribute to membrane biophysical properties and are involved in cellular differentiation, recognition, and mediating interactions. The described nanoHPLC-ESI-Q/ToF methodology utilizes known biosynthetic pathways, accurate mass detection, optimized collision-induced disassociation, and a robust nanoflow chromatographic separation for the analysis of intact sphingolipids found in human tissue, cells, and serum. The methodology was developed and validated with an emphasis on addressing the common issues experienced in profiling these amphipathic lipids, which are part of the glycocalyx and lipidome. The high sensitivity obtained using nanorange flow rates with robust chromatographic reproducibility over a wide range of concentrations and injection volumes results in confident identifications for profiling these low-abundant biomolecules.

DOI: https://doi.org/10.1021/acs.analchem.4c00077
Forensic Toxicol. 2024 Apr 01.

Development of an LC-MS/MS method for the determination of five psychoactive drugs in postmortem urine by optimization of enzymatic hydrolysis of glucuronide conjugates.

Tomohito Matsuo, Tadashi Ogawa, Masae Iwai, Katsutoshi Kubo, Fumio Kondo, Hiroshi Seno.

   PURPOSE: Toxicological analyses of biological samples play important roles in forensic and clinical investigations. Ingested drugs are excreted in urine as conjugates with endogenous substances such as glucuronic acid; hydrolyzing these conjugates improves the determination of target drugs by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this study, we sought to improve the enzymatic hydrolysis of glucuronide conjugates of five psychoactive drugs (11-nor-9-carboxy-Δ9-tetrahydrocannabinol, oxazepam, lorazepam, temazepam, and amitriptyline).
METHODS: The efficiency of enzymatic hydrolysis of glucuronide conjugates in urine was optimized by varying temperature, enzyme volume, and reaction time. The hydrolysis was performed directly on extraction columns. This analysis method using LC-MS/MS was applied to forensic autopsy samples after thorough validation.
RESULTS: We found that the recombinant β-glucuronidase B-One® quantitatively hydrolyzed these conjugates within 3 min at room temperature directly on extraction columns. This on-column method saved time and eliminated the loss of valuable samples during transfer to the extraction column. LC-MS/MS-based calibration curves processed with this method showed good linearity, with r2 values exceeding 0.998. The intra- and inter-day accuracies and precisions of the method were 93.0-109.7% and 0.8-8.8%, respectively. The recovery efficiencies were in the range of 56.1-104.5%. Matrix effects were between 78.9 and 126.9%.
CONCLUSIONS: We have established an LC-MS/MS method for five psychoactive drugs in urine after enzymatic hydrolysis of glucuronide conjugates directly on extraction columns. The method was successfully applied to forensic autopsy samples. The established method will have broad applications, including forensic and clinical toxicological investigations.

Keywords:  Glucuronide conjugates; Hydrolysis; LC–MS/MS; Postmortem urine; Psychoactive drugs; β-glucuronidase

DOI:  https://doi.org/10.1007/s11419-024-00685-1
Se Pu. 2024 Apr;42(4): 345-351

[Determination of adenosine content in heart tissue by ultra performance liquid chromatography-triple quadrupole mass spectrometry].

Zuoyin Zhu, Wenbo Guo, Hanke Zhao, Jie Wang, Junhua Yang, Xinli Zhou.

  A method based on ultra performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-MS/MS) was developed and validated for the rapid and accurate determination of adenosine (Ado) in cardiac tissues with high sensitivity and specificity. The samples were dissolved in 1 mL of ultrapure water containing 10 μmol/L 2-hydroxy-3-nonyladenine hydrochloride (EHNA) as a stabilizer, ground at low temperature for 2 min, and then ultrasonically extracted at 60 Hz in an ice-water bath for 40 min. Methanol and 5 mmol/L ammonium acetate solution were used as the mobile phases under a flow rate of 0.4 mL/min, a column temperature of 40 ℃ and an injection volume of 3 μL. The Ado in cardiac tissue was qualitatively and quantitatively analyzed by electrospray ionization (ESI) positive-ion-switching in multiple reaction monitoring (MRM) mode. A solvent standard curve and the external standard method were used for the accurate quantification of Ado. The results showed that the matrix effect of Ado in cardiac tissue was very low. A good linear relationship was obtained in the range of 0.1-160 ng/mL, and the correlation coefficient (r2) was 0.9930. The limits of detection (LOD) and quantification (LOQ) were 0.03 and 0.1 ng/mL, respectively. The spiked recoveries of Ado in murine cardiac tissue were 113.6%, 96.3%, and 102.9% at three spiked levels of low, medium, and high, respectively. The intra-day repeatability (RSDs) were 1.7%-8.4%, and the inter-day reproducibility (RSDs) were 2.6%-7.4%. Based on the correlation and consistency results, a positive bias was observed between the proposed UPLC-MS/MS method and the double-antibody sandwich method. Moreover, the Ado contents detected by these two methods were significantly positively correlated (P<0.0001). Cardiac tissue samples were collected from 17 mice and 17 rats and detected in our laboratory. The content ranges of Ado in the cardiac tissues of mice and rats determined by the developed UPLC-MS/MS method were 3.25-8.78 mg/kg and 10.24-15.19 mg/kg, respectively (average adenosine contents: 5.37 and 12.60 mg/kg, respectively). The developed method is simple, accurate, sensitive, and it is suitable for the determination of Ado in cardiac tissues. It also provides important technical support for cardiac clinical research and disease diagnosis.

Keywords:  adenosine (Ado); cardiac tissue; ultra performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-MS/MS)

DOI:  https://doi.org/10.3724/SP.J.1123.2023.09016
J Sep Sci. 2024 Apr;47(7): e2300763

Simultaneous determination of folic acid photolysis products and oxidized guanine derivatives in plasma by liquid chromatography-tandem mass spectrometry.

Juan Li, Wenchao Hu, Mengxue Liu, Yingqi Tian, Manni He, Hongmin Liu.

  Folic acid (FA) is easily photodegraded to yield 6-formylpterin and pterin-6-carboxylic acid, which can generate reactive oxygen species and result in the formation of oxidized guanine derivatives such as 8-hydroxy-2'-deoxyguanosine and 8-hydroxy-guanosine. In this study, we developed a simple, rapid, and sensitive liquid chromatography-tandem mass spectrometry strategy for the simultaneous determination of FA photolysis products and oxidized guanine derivatives in plasma samples. Chromatographic separation was performed on a Waters HSS T3 column (2.1 × 100 mm, 5.0 μm) with gradient elution at a flow rate of 0.25 mL/min. Plasma samples were first pretreated with 1% formic acid, followed by protein precipitation with methanol. The developed method showed good linear relationships between 1 and 2000 ng/mL (r2 > 0.99). The intra- and inter-day precisions ranged from 2.6% to 7.5% and from 2.5% to 6.5%, respectively. Recoveries of the analytes were between 75.4% and 112.4% with the relative standard deviation < 9.1%. Finally, the method was applied to quantify FA photolysis products and oxidized guanine derivatives in rats with light and non-light conditions.

Keywords:  folic acid; liquid chromatography‐tandem mass spectrometry; oxidized guanine derivatives; photolysis products; rat plasma

DOI:  https://doi.org/10.1002/jssc.202300763
Bioinformatics. 2024 Apr 01. pii: btae174. [Epub ahead of print]

The IDSM mass spectrometry extension: searching mass spectra using SPARQL.

Jakub Galgonek, Jiří Vondrášek.

SUMMARY: The Integrated Database of Small Molecules (IDSM) integrates data from small-molecule datasets, making them accessible through the SPARQL query language. Its unique feature is the ability to search for compounds through SPARQL based on their molecular structure. We extended IDSM to enable mass spectra databases to be integrated and searched for based on mass spectrum similarity. As sources of mass spectra, we employed the MassBank of North America (MoNA) database and the In Silico Spectral Database (ISDB) of natural products.
AVAILABILITY AND IMPLEMENTATION: The extension is an integral part of IDSM, which is available at https://idsm.elixir-czech.cz. The manual and usage examples are available at https://idsm.elixir-czech.cz/docs/ms. The source codes of all IDSM parts are available under open-source licences at https://github.com/idsm-src.

DOI: https://doi.org/10.1093/bioinformatics/btae174
J Chromatogr A. 2024 Mar 21. pii: S0021-9673(24)00191-2. [Epub ahead of print]1721 464818

In-silico method development and optimization of on-line comprehensive two-dimensional liquid chromatography via a shortcut model.

Monica Tirapelle, Dian Ning Chia, Fanyi Duanmu, Maximilian O Besenhard, Luca Mazzei, Eva Sorensen.

  Comprehensive two-dimensional liquid chromatography (LCxLC) represents a valuable alternative to conventional single column, or one-dimensional, liquid chromatography (1D-LC) for resolving multiple components in a complex mixture in a short time. However, developing LCxLC methods with trial-and-error experiments is challenging and time-consuming, which is why the technique is not dominant despite its significant potential. This work presents a novel shortcut model to in-silico predicting retention time and peak width within an RPLCxRPLC separation system (i.e., LCxLC systems that use reversed-phase columns (RPLC) in both separation dimensions). Our computationally effective model uses the hydrophobic-subtraction model (HSM) to predict retention and considers limitations due to the sample volume, undersampling and the maximum pressure drop. The shortcut model is used in a two-step strategy for sample-dependent optimization of RPLCxRPLC separation systems. In the first step, the Kendall's correlation coefficient of all possible combinations of available columns is evaluated, and the best column pair is selected accordingly. In the second step, the optimal values of design variables, flow rate, pH and sample loop volume, are obtained via multi-objective stochastic optimization. The strategy is applied to method development for the separation of 8, 12 and 16 component mixtures. It is shown that the proposed strategy provides an easy way to accelerate method development for full-comprehensive 2D-LC systems as it does not require any experimental campaign and an entire optimization run can take less than two minutes.

Keywords:  2D resolution; In-silico method development; Multi-objective optimization; Stochastic optimization; Two-dimensional liquid chromatography

DOI:  https://doi.org/10.1016/j.chroma.2024.464818