bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2024‒08‒11
sixteen papers selected by
Sofia Costa, Matterworks
  1. Analysis types and quantification methods applied in UHPLC-MS metabolomics research: a tutorial.
  2. Development and Validation of a Sensitive Liquid Chromatography-Tandem Mass Spectrometry Method for Therapeutic Drug Monitoring of Ceftolozane and Tazobactam in Human Plasma Microsamples.
  3. Validation of a method for the determination of Aderamastat (FP-025) in K2EDTA human plasma by LC-MS/MS.
  4. Rapid Analysis of Glucosinolates Using Direct-Infusion Mass Spectrometry.
  5. Fungicide Metabolite MS2 Spectral Libraries for Comprehensive Human Biomonitoring.
  6. Liquid chromatography-mass spectrometry quantification of phytochemicals in Withania somnifera using data-dependent acquisition, multiple-reaction-monitoring, and parallel-reaction-monitoring with an inclusion list.
  7. Detection and quantification of selected cannabinoids in oral fluid samples by protein precipitation and LC-MS/MS.
  8. Desorption Electrospray Ionization Cyclic Ion Mobility-Mass Spectrometry Imaging for Traumatic Brain Injury Spatial Metabolomics.
  9. Development and validation of a liquid chromatography-tandem mass spectrometry method for the determination of polymixin B1, B2, ile-B1, E1, and E2 in human plasma and its clinical pharmacokinetic application.
  10. Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer.
  11. Software-assisted automated detection and identification of "unknown" analogues of benzodiazepines in liquid chromatography mass spectrometry analysis.
  12. Trace detection of styphnate from pre- and post-blast samples by hydrophilic interaction chromatography with tandem mass spectrometry.
  13. Elucidating of the metabolic impact of risperidone on brain microvascular endothelial cells using untargeted metabolomics-based LC-MS.
  14. Simultaneous Determination of Ripretinib and Its Desmethyl Metabolite in Human Plasma Using LC-MS/MS.
  15. Quantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals.
  16. Natural Products Dereplication: Databases and Analytical Methods.
  1. Metabolomics. 2024 Aug 07. 20(5): 95
    Analysis types and quantification methods applied in UHPLC-MS metabolomics research: a tutorial.
    Richard D Beger, Royston Goodacre, Christina M Jones, Katrice A Lippa, Oleg A Mayboroda, Donna O'Neill, Lukas Najdekr, Ioanna Ntai, Ian D Wilson, Warwick B Dunn.
      BACKGROUND: Different types of analytical methods, with different characteristics, are applied in metabolomics and lipidomics research and include untargeted, targeted and semi-targeted methods. Ultra High Performance Liquid Chromatography-Mass Spectrometry is one of the most frequently applied measurement instruments in metabolomics because of its ability to detect a large number of water-soluble and lipid metabolites over a wide range of concentrations in short analysis times. Methods applied for the detection and quantification of metabolites differ and can either report a (normalised) peak area or an absolute concentration.AIM OF REVIEW: In this tutorial we aim to (1) define similarities and differences between different analytical approaches applied in metabolomics and (2) define how amounts or absolute concentrations of endogenous metabolites can be determined together with the advantages and limitations of each approach in relation to the accuracy and precision when concentrations are reported.
    KEY SCIENTIFIC CONCEPTS OF REVIEW: The pre-analysis knowledge of metabolites to be targeted, the requirement for (normalised) peak responses or absolute concentrations to be reported and the number of metabolites to be reported define whether an untargeted, targeted or semi-targeted method is applied. Fully untargeted methods can only provide (normalised) peak responses and fold changes which can be reported even when the structural identity of the metabolite is not known. Targeted methods, where the analytes are known prior to the analysis, can also report fold changes. Semi-targeted methods apply a mix of characteristics of both untargeted and targeted assays. For the reporting of absolute concentrations of metabolites, the analytes are not only predefined but optimized analytical methods should be developed and validated for each analyte so that the accuracy and precision of concentration data collected for biological samples can be reported as fit for purpose and be reviewed by the scientific community.
    Keywords:  Metabolomics; Quantification; Semi-targeted; Targeted; UHPLC-MS; Untargeted; Validation
    DOI:  https://doi.org/10.1007/s11306-024-02155-6
  2. Ther Drug Monit. 2024 Aug 06.
    Development and Validation of a Sensitive Liquid Chromatography-Tandem Mass Spectrometry Method for Therapeutic Drug Monitoring of Ceftolozane and Tazobactam in Human Plasma Microsamples.
    Matteo Conti, Beatrice Giorgi, Milo Gatti, Pierluigi Viale, Federico Pea.
      BACKGROUND: Ceftolozane/tazobactam (C-T) is a novel beta-lactam/beta-lactamase inhibitor combination approved for the treatment of various infections caused by difficult-to-treat Pseudomonas aeruginosa. In critically ill patients, C-T may exhibit significant pharmacokinetic variability, both between individuals and within individuals, warranting therapeutic drug monitoring for clinical purposes. We aim to develop and validate a novel and sensitive analytical method for concurrently determining C and T in human plasma microsamples (3 μL).METHODS: The method was developed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with positive electrospray ionization and multiple reaction monitoring (MRM) detection modes, employing specific mass transitions for both drugs. Sample preparation was simple, and the chromatographic run lasted only 4 minutes. Validation was conducted according to European Medicines Agency (EMA) guidelines, encompassing specificity, sensitivity, linearity, precision, accuracy, matrix effect, extraction recovery, limit of quantification, and drug stability. The validated method was applied to measure C and T in 32 plasma samples collected from critically ill patients with multidrug-resistant, gram-negative, bacterial infections.
    RESULTS: The method ensured accurate (BIAS% 2.1-9.6 for C and -2.2 to 15.2 for T) and precise intraday CV% for C: 6.7-5.5; for T: 1.3-8.9; interday CV% for C 6.0-10.8; for T 4.1-10.2) measurements of C-T over a wide concentration range (0.2-200.0 mg/L for C and 0.1-100.0 mg/L for T). Overall, the recovery at quality control concentration levels was high for both C and T (mean values: 90-91 for C and 89-92 for T). Analyte stability was satisfactory in both human plasma and extracts under various storage conditions. The clinical applicability of the assay was confirmed by the reliably quantifying C and T in clinical plasma samples.
    CONCLUSIONS: The developed and validated LC-MS/MS method is sensitive and suitable for monitoring C and T in human plasma microsamples.
    DOI:  https://doi.org/10.1097/FTD.0000000000001236
  3. J Chromatogr B Analyt Technol Biomed Life Sci. 2024 Jul 18. pii: S1570-0232(24)00253-8. [Epub ahead of print]1245 124244
    Validation of a method for the determination of Aderamastat (FP-025) in K2EDTA human plasma by LC-MS/MS.
    Khalid S Abd-Elaziz, Rex Cheng, Joe Chen, Hans Maarse, Yisheng Lee, Wenjin Yang, Benjamin Chien, Zuzana Diamant, Jos Kosterink, Daniël J Touw.
      Aderamastat (FP-025) is a small molecule, selective matrix metalloproteinase (MMP)-12 inhibitor, under development for respiratory conditions which may include chronic inflammatory airway diseases and pulmonary fibrosis. To support evaluation of the pharmacokinetic parameters of Aderamastat in humans, we developed and validated a high-performance liquid chromatography tandem mass spectrometry (LC-MS/MS) analytical method for the quantification of Aderamastat in human plasma. This assay was validated in compliance with the Food and Drug Administration (FDA) Good Laboratory Practice Regulations (GLP) and European Medicines Agency (EMA) guidelines. K2EDTA human plasma samples were spiked with internal standard, processed by liquid-liquid extraction, and analyzed using reversed-phase HPLC with Turbo Ion Spray® MS/MS detection. Separation was done using a chromatographic gradient on 5 µm C6-Phenyl 110 Å, 50*2 mm analytical column at a temperature of 35 °C. The LC-MS/MS bioanalytical method, developed by QPS Taiwan to determine the concentration of Aderamastat in K2EDTA human plasma, was successfully validated with respect to linearity, sensitivity, accuracy, precision, dilution, selectivity, hemolyzed plasma, lipemic plasma, batch size, recovery, matrix effect, and carry-over. These data indicate that the method for determination of Aderamastat concentrations in human K2EDTA plasma can be used in pharmacokinetics studies and subsequent clinical trials with Aderamastat. Authors declare that, this novel data is not published and not under consideration for publication by another journal than this journal. All data will be made available on request.
    Keywords:  Aderamastat; Bioanalysis Assay; FP-025; LC-MS/MS; Matrix Metalloproteinase (MMP)-12 inhibitor; Validation
    DOI:  https://doi.org/10.1016/j.jchromb.2024.124244
  4. Mass Spectrom (Tokyo). 2024 ;13(1): A0150
    Rapid Analysis of Glucosinolates Using Direct-Infusion Mass Spectrometry.
    Miho Tanewata, Akira Oikawa.
      We developed a rapid, accurate, and quantitative method for analyzing glucosinolates (GSLs) by combining column-free liquid chromatography (LC) with direct-infusion mass spectrometry (MS). Conventional methods for analyzing GSLs take a long time (20-50 min per sample) to perform compound separation on an LC column. We achieved a shortened analysis time of 30 seconds per sample using a direct-infusion method. Samples were continuously injected by a pump and autosampler on an LC system directly into the MS. Orbitrap MS detected 11 types of GSLs in the extracts of turnip hypocotyls. The calibration curve of a GSL standard showed a linear response over a 6-digit concentration range from 1 nM to 1 mM. In addition, no decrease in the detected intensity of GSL ions in 100 continuous analyses of turnip extracts was observed. This method may be applied for rapid analysis of GSLs and other health-functional or bioactive compounds.
    Keywords:  orbitrap MS; solid phase extraction; turnip
    DOI:  https://doi.org/10.5702/massspectrometry.A0150
  5. J Agric Food Chem. 2024 Aug 05.
    Fungicide Metabolite MS2 Spectral Libraries for Comprehensive Human Biomonitoring.
    Romanas Chaleckis, Yuki Ito, Hitomi Wasada, Craig E Wheelock, Hisashi Oishi, Motohiro Tomizawa, Michihiro Kamijima.
      Fungicides undergo rapid metabolism and are excreted in the urine. There are few methods for screening these ubiquitous compounds, which have a high potential for human exposure. High-resolution mass spectrometry (HRMS) is a suitable technique to assess fungicide exposures; however, there is a lack of spectral libraries for fungicide annotation and in particular for downstream metabolites. We created spectral libraries for 32 fungicides for suspect screening. Fungicide standards were administered to mice, and 24-h urine was analyzed using hydrophilic interaction and reversed-phase chromatography coupled to hybrid quadrupole-orbitrap mass spectrometry. Suspect metabolite MS2 spectra for library creation were selected based on the ratio of exposed-to-control mouse urine. MS2 libraries were applied to urine collected from female university students (n = 73). Several tetraconazole and tebuconazole metabolites were detected in 3% (2/73) of the samples. The creation of comprehensive suspect screening MS2 libraries is a useful tool to detect fungicide exposure for human biomonitoring.
    Keywords:  MS2 library; pesticide; suspect screening; tebuconazole; untargeted measurements; urine
    DOI:  https://doi.org/10.1021/acs.jafc.4c02339
  6. Front Chem. 2024 ;12 1373535
    Liquid chromatography-mass spectrometry quantification of phytochemicals in Withania somnifera using data-dependent acquisition, multiple-reaction-monitoring, and parallel-reaction-monitoring with an inclusion list.
    Luke C Marney, Jaewoo Choi, Armando Alcazar Magana, Liping Yang, Natascha Techen, Md Nure Alam, Mikah Brandes, Amala Soumyanath, Jan F Stevens, Claudia S Maier.
      Characterization of botanical extracts by mass spectrometry-based metabolomics analysis helps in determining the phytochemical composition that underlies their bioactivity and potential health benefits, while also supporting reproducibility of effects in clinical trials. The quantification of seven withanolides in Withania somnifera using three mass-spectrometry methods was evaluated using Deming regression. Two high-resolution time-of-flight mass spectrometry methods were used, one operating in data-dependent acquisition mode and the other in parallel-reaction-monitoring mode with an inclusion list. The two high-resolution time-of-flight mass spectrometry methods were compared to a multiple-reaction-monitoring method. We evaluated in-source fragmentation of steroidal glycosides and optimized the methods accordingly. A novel software approach to integrating parallel-reaction-monitoring data acquired with an inclusion list was developed. Combining and comparing quantitative results allowed for quantitative specificity, good precision, and adjustment of instrument source conditions for optimal quantification by multiple-reaction-monitoring mass spectrometry, an analytical method that is widely accessible in analytical and phytochemical laboratories.
    Keywords:  Withania somnifera; ashwagandha; deming regression; mass spectrometry; metabolomics; method comparison; withanolides
    DOI:  https://doi.org/10.3389/fchem.2024.1373535
  7. Forensic Sci Int. 2024 Jul 29. pii: S0379-0738(24)00255-X. [Epub ahead of print]363 112174
    Detection and quantification of selected cannabinoids in oral fluid samples by protein precipitation and LC-MS/MS.
    Mónica Antunes, Susana Simões, Suzana Fonseca, João Franco, Eugenia Gallardo, Mário Barroso.
      Cannabis is the most widely consumed illicit drug worldwide. As consumption rates increase, partially due to the decriminalization of its use for medicinal and recreational purposes, analytical methods for monitoring different cannabinoids in several biological matrices have been developed. Herein, a simple and fast extraction procedure to extract natural cannabinoids from oral fluid (OF) samples was developed and fully validated according to the ANSI/ASB 2019 Standard Practices for Method Validation in Forensic Toxicology. Using only 0.2 mL of neat OF, the analytes [Δ9-tetrahidrocannabinol (THC), 11-hydroxy-Δ9-tetrahydrocannabinol (THC-OH), 11-nor-9-carboxy-Δ9-tetrahydrocannabinol (THC-COOH), cannabinol (CBN) and cannabidiol (CBD)] were extracted by protein precipitation with a mixture of methanol:acetonitrile (80:20, v/v); the extracts were centrifuged, evaporated to dryness and reconstituted in 100 µL of methanol. Analysis was performed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The developed methodology produced linear results for all compounds, with working ranges of 0.1-50 ng/mL for THC, 0.5-50 ng/mL for THC-OH, CBN and CBD, and 0.05-1 ng/mL for THC-COOH. Ion suppression was observed for THC, CBN and CBD, which did not impair sensitivity considering the low limits of quantification (LOQs) and limits of detection (LODs) obtained (which varied between 0.05 and 0.5 ng/mL). The extraction procedure produced great recoveries, and the compounds were stable. No interferences were found, and the method proved to be extremely fast, selective, precise, and accurate for use in routine analysis. The method was successfully applied to authentic samples.
    Keywords:  Cannabinoids; LC–MS/MS; Oral fluid; Protein precipitation
    DOI:  https://doi.org/10.1016/j.forsciint.2024.112174
  8. Anal Chem. 2024 Aug 06.
    Desorption Electrospray Ionization Cyclic Ion Mobility-Mass Spectrometry Imaging for Traumatic Brain Injury Spatial Metabolomics.
    Dmitry Leontyev, Hernando Olivos, Bindesh Shrestha, Pooja M Datta Roy, Michelle C LaPlaca, Facundo M Fernández.
      Lipidomics focuses on investigating alterations in a wide variety of lipids that harness important information on metabolic processes and disease pathology. However, the vast structural diversity of lipids and the presence of isobaric and isomeric species creates serious challenges in feature identification, particularly in mass spectrometry imaging experiments that lack front-end separations. Ion mobility has emerged as a potential solution to address some of these challenges and is increasingly being utilized as part of mass spectrometry imaging platforms. Here, we present the results of a pilot mass spectrometry imaging study on rat brains subjected to traumatic brain injury (TBI) to evaluate the depth and quality of the information yielded by desorption electrospray ionization cyclic ion mobility mass spectrometry (DESI cIM MSI). Imaging data were collected with one and six passes through the cIM cell. Increasing the number of passes increased the ion mobility resolving power and the resolution of isobaric lipids, enabling the creation of more specific maps. Interestingly, drift time data enabled the recognition of multiply charged phosphoinositide species in the complex data set generated. These species have not been previously reported in TBI MSI studies and were found to decrease in the hippocampus region following injury. These changes were attributed to increased enzymatic activity after TBI, releasing arachidonic acid that is converted to eicosanoids to control inflammation. A substantial reduction in NAD and alterations in other adenine metabolites were also observed, supporting the hypothesis that energy metabolism in the brain is severely disrupted in TBI.
    DOI:  https://doi.org/10.1021/acs.analchem.4c02394
  9. J Pharm Biomed Anal. 2024 Aug 06. pii: S0731-7085(24)00443-6. [Epub ahead of print]250 116403
    Development and validation of a liquid chromatography-tandem mass spectrometry method for the determination of polymixin B1, B2, ile-B1, E1, and E2 in human plasma and its clinical pharmacokinetic application.
    Dong Xiang, Ninghong Li, Guangjie Yang, Hengyi Yu, Xiping Li, Lihui Qiu, Yufei Chen, Lu Liu, Xuepeng Gong.
      Polymyxin B (PB) and Polymyxin E (PE, also called colistin) are used as the last treatment resort for multidrug-resistant Gram-negative bacterial infections. The nephrotoxicity and neurotoxicity of polymyxins limit their clinical use, and guidelines recommend therapeutic drug monitoring (TDM) to optimize efficacy and reduce toxicity. However, there are limited analytical methods available for the determination of PB and PE. This study aimed to develop a simple and robust liquid chromatography with tandem mass spectrometry (LC-MS/MS) analytical method for determining the main compounds of PB and PE, namely PB1, PB2, ile-PB1, PE1, and PE2, in human plasma and to investigate of their pharmacokinetics in critically ill patients with the use of PB and PE, respectively. Plasma PB1, PB2, ile-PB1, PE1, and PE2 were chromatographically separated on a Welch LP-C18 column and detected using electrospray ionization mode coupled with multiple reaction monitoring. The calibration curve showed acceptable linearity over 20-10,000 ng/mL for PB1, PE1, and PE2 and 10-5000 ng/mL for PB2 and ile-PB1 in the plasma, respectively. After validation following approved guidelines, this method was successfully applied for PB and PE pharmacokinetic analysis and TDM in critically ill patients. Additionally, the composition of PB1, PB2, ile-PB1, PE1, and PE2 remains unchanged from 0 to 12 h after entering the patient's body.
    Keywords:  LC-MS/MS; Method development; Pharmacokinetic study; Polymyxin B; Polymyxin E
    DOI:  https://doi.org/10.1016/j.jpba.2024.116403
  10. Res Sq. 2024 Jul 25. pii: rs.3.rs-4758843. [Epub ahead of print]
    Denoising Search doubles the number of metabolite and exposome annotations in human plasma using an Orbitrap Astral mass spectrometer.
    Oliver Fiehn, Fanzhou Kong, Tong Shen, Yuanyue Li, Amer Bashar, Susan Bird.
      Chemical exposures may impact human metabolism and contribute to the etiology of neurodegenerative disorders like Alzheimer's Disease (AD). Identifying these small metabolites involves matching experimental spectra to reference spectra in databases. However, environmental chemicals or physiologically active metabolites are usually present at low concentrations in human specimens. The presence of noise ions can significantly degrade spectral quality, leading to false negatives and reduced identification rates. In response to this challenge, the Spectral Denoising algorithm removes both chemical and electronic noise. Spectral Denoising outperformed alternative methods in benchmarking studies on 240 tested metabolites. It improved high confident compound identifications at an average 35-fold lower concentrations than previously achievable. Spectral Denoising proved highly robust against varying levels of both chemical and electronic noise even with >150-fold higher intensity of noise ions than true fragment ions. For human plasma samples of AD patients that were analyzed on the Orbitrap Astral mass spectrometer, Denoising Search detected 2.3-fold more annotated compounds compared to the Exploris 240 Orbitrap instrument, including drug metabolites, household and industrial chemicals, and pesticides. This combination of advanced instrumentation with a superior denoising algorithm opens the door for precision medicine in exposome research.
    DOI:  https://doi.org/10.21203/rs.3.rs-4758843/v1
  11. Rapid Commun Mass Spectrom. 2024 Oct 15. 38(19): e9883
    Software-assisted automated detection and identification of "unknown" analogues of benzodiazepines in liquid chromatography mass spectrometry analysis.
    Dana Marder, Ori Gutman, Uriel Bretler, Yiffat Katz, Lilach Yishai-Aviram, Eyal Drug.
      RATIONALE: Benzodiazepines (BZDs) construct a large group of psychoactive drugs acting as depressants of the central nervous system (CNS) and used in medicine as sedatives and anxiolytic and antiepileptic agents. The illicit use of these materials is a worldwide problem, and for many years, part of the benzodiazepines have been abused as rape drugs. For example, flunitrazepam (Rohypnol) is most commonly linked by media reports to drug-facilitated sexual assaults, more commonly referred to as "date rape." Furthermore, there are growing concerns for other misuses of these drugs. Over the last few years, there was an increase in the number, type, and availability of new psychoactive substances (NPS) belonging to the benzodiazepine group, challenging standard forensic labs to fully identify the chemical structure of new, unknown benzodiazepines.METHODS: This work demonstrates a new application of the automated tool for the detection and identification of benzodiazepine analogues using high-resolution-accurate-mass LC-MS analysis, followed by "Compound Discoverer" (CD) software data processing, to automatically detect various benzodiazepine analogues by picking peaks and compare them to in silico calculated modifications made on a predefined basic backbone. Subsequently, a complete structural elucidation for the proposed molecular formula is obtained by MS/MS data analysis of the suspected component.
    RESULTS: This method was found to be useful for the automated detection and putative identification of a series of nine "unknown" benzodiazepine analogues, at concentrations in the low ng/mL range.
    CONCLUSIONS: We hereby present a general demonstration of this powerful tool for the forensic community in the detection and identification of hazardous unknown compounds.
    DOI:  https://doi.org/10.1002/rcm.9883
  12. Rapid Commun Mass Spectrom. 2024 Oct 15. 38(19): e9882
    Trace detection of styphnate from pre- and post-blast samples by hydrophilic interaction chromatography with tandem mass spectrometry.
    Sarah N Sipe, Courtney A Cruse, Christopher A Tipple, Mark L Miller.
      RATIONALE: Although ubiquitous in explosives and ammunition, few trace methods for detection of heavy metal-containing primary explosives from forensic samples are currently in practice.METHODS: Extracts of cotton swabs or direct sampling of items were cleaned up using solid-phase extraction to remove heavy metal contaminants (i.e., lead) while retaining the organic styphnate component. The styphnate was chromatographically separated using hydrophilic interaction chromatography (HILIC) and detected via high-resolution tandem mass spectrometry (MS/MS) using a sensitive, targeted approach in five minutes or less.
    RESULTS: A mass spectrometric method for the detection of styphnate, including limit of detection (LOD), sample stability, and interferences was developed. We present a validated method for the extraction, separation, and detection of styphnate from lead(II) styphnate with an estimated LOD of 257 ppt (pg/mL).
    CONCLUSIONS: We detail an improved LOD relative to previous reports for trace detection of styphnate and, for the first time to our knowledge, the post-blast analysis of styphnate.
    DOI:  https://doi.org/10.1002/rcm.9882
  13. Toxicol Rep. 2024 Dec;13 101691
    Elucidating of the metabolic impact of risperidone on brain microvascular endothelial cells using untargeted metabolomics-based LC-MS.
    Surachai Ngamratanapaiboon, Napatarin Srikornvit, Patipol Hongthawonsiri, Krittaboon Pornchokchai, Siriphattarinya Wongpitoonmanachai, Jiajun Mo, Petchlada Pholkla, Pracha Yambangyang, Phichanan Duchda, Jenyuk Lohwacharin, Watcharaporn Devakul Na Ayutthaya.
      Risperidone is useful for the treatment of schizophrenia symptoms; however, it also has side effects, and an overdose can be harmful. The metabolic effects of risperidone at high therapeutic doses and its metabolites have not been elucidated. Endogenous cellular metabolites may be comprehensively analyzed using untargeted metabolomics-based liquid chromatography-mass spectrometry (LC-MS), which can reveal changes in cell regulation and metabolic pathways. By identifying the metabolites and pathway changes using a nontargeted metabolomics-based LC-MS approach, we aimed to shed light on the potential toxicological effects of high-dose risperidone on brain microvascular endothelial cells (MVECs) associated with the human blood brain barrier. A total of 42 metabolites were selected as significant putative metabolites of the toxicological response of high-dose risperidone in MVECs. Six highly correlated pathways were identified, including those involving diacylglycerol, fatty acid, ceramide, glycerophospholipid, amino acid, and tricarboxylic acid metabolism. We demonstrated that methods focused on metabolomics are useful for identifying metabolites that may be used to clarify the mechanism of drug-induced toxicity.
    Keywords:  Brain microvascular endothelial cells; Liquid chromatography-mass spectrometry; Risperidone; Untargeted metabolomics
    DOI:  https://doi.org/10.1016/j.toxrep.2024.101691
  14. Ther Drug Monit. 2024 Aug 06.
    Simultaneous Determination of Ripretinib and Its Desmethyl Metabolite in Human Plasma Using LC-MS/MS.
    Zhou-Yi Qian, Ping Wang, Zi-Yi Wang, Yang Zhao, Tian-Tian Du, Hao Xu, Yong-Qing Wang, Lu-Ning Sun.
      BACKGROUND: Ripretinib, a recently developed tyrosine kinase inhibitor with switch-control abilities, can inhibit both primary and secondary activation of KIT(KIT proto-oncogene receptor tyrosine kinase) and platelet-derived growth factor receptor alpha (PDGFRA) mutants, which contribute to gastrointestinal stromal tumor progression.METHODS: In this study, a high-performance liquid chromatography-tandem mass spectrometry method to measure the concentrations of ripretinib and its active desmethyl metabolite DP-5439 in human plasma was developed and validated. Plasma samples were extracted and recovered by precipitation with acetonitrile containing the internal standard and diluted with acetonitrile before analysis. Ripretinib and DP-5439 were separated using chromatography on a Waters ACQUITY UPLC HSS T3 column (2.1 mm × 50 mm, 1.8 μm) with gradient elution using 0.1% formic acid and 5 mM ammonium formate in water as mobile phase A and acetonitrile as mobile phase B. The mobile phase was set to a flow rate of 0.5 mL/min.
    RESULTS: The calibration curves were linear across the following concentration range: 7.5 to 3000 ng/mL for ripretinib and 10 to 4000 ng/mL for DP-5439. The intraday and interday precisions were approximately 15% for all analytes in the quality control samples. The relative matrix effects in extracted plasma samples (90.3%-108.8% at different levels) were considered acceptable.
    CONCLUSIONS: This method will be a useful tool in oncology to facilitate the further clinical development of ripretinib.
    DOI:  https://doi.org/10.1097/FTD.0000000000001245
  15. Anal Chem. 2024 Aug 07.
    Quantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals.
    Helge Hecht, Wudmir Y Rojas, Zargham Ahmad, Aleš Křenek, Jana Klánová, Elliott J Price.
      There is a lack of experimental electron ionization high-resolution mass spectra available to assist compound identification. The in silico generation of mass spectra by quantum chemistry can aid annotation workflows, in particular to support the identification of compounds that lack experimental reference spectra, such as environmental chemicals. We present an open-source, semiautomated workflow for the in silico prediction of electron ionization high-resolution mass spectra at 70 eV based on the QCxMS software. The workflow was applied to predict the spectra of 367 environmental chemicals, and the accuracy was evaluated by comparison to experimental reference spectra acquired. The molecular flexibility, number of rotatable bonds, and number of electronegative atoms of a compound were negatively correlated with prediction accuracy. Few analytes are predicted to sufficient accuracy for the direct application of predicted spectra in spectral matching workflows (overall average score 428). The m/z values of the top 5 most abundant ions of predicted spectra rarely match ions in experimental spectra, evidencing the disconnect between simulated fragmentation pathways and empirical reaction mechanisms.
    DOI:  https://doi.org/10.1021/acs.analchem.4c02589
  16. Prog Chem Org Nat Prod. 2024 ;124 1-56
    Natural Products Dereplication: Databases and Analytical Methods.
    Ignacio Pérez-Victoria.
      The development of efficient methods for dereplication has been critical in the re-emergence of the research in natural products as a source of drug leads. Current dereplication workflows rapidly identify already known bioactive secondary metabolites in the early stages of any drug discovery screening campaign based on natural extracts or enriched fractions. Two main factors have driven the evolution of natural products dereplication over the last decades. First, the availability of both commercial and public large databases of natural products containing the key annotations against which the biological and chemical data derived from the studied sample are searched for. Second, the considerable improvement achieved in analytical technologies (including instrumentation and software tools) employed to obtain robust and precise chemical information (particularly spectroscopic signatures) on the compounds present in the bioactive natural product samples. This chapter describes the main methods of dereplication, which rely on the combined use of large natural product databases and spectral libraries, alongside the information obtained from chromatographic, UV-Vis, MS, and NMR spectroscopic analyses of the samples of interest.
    Keywords:  Chromatography; Databases; Dereplication; Mass spectrometry; Natural products; Nuclear magnetic resonance spectroscopy; Spectral libraries; Structural features; Taxonomy; Ultraviolet–Visible spectroscopy
    DOI:  https://doi.org/10.1007/978-3-031-59567-7_1
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