bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒05‒28
thirty-one papers selected by
Sofia Costa

  1. Anal Bioanal Chem. 2023 May 25.
      In mass spectrometry (MS)-based metabolomics, there is a great need to combine different analytical separation techniques to cover metabolites of different polarities and apply appropriate multi-platform data processing. Here, we introduce AriumMS (augmented region of interest for untargeted metabolomics mass spectrometry) as a reliable toolbox for multi-platform metabolomics. AriumMS offers augmented data analysis of several separation techniques utilizing a region-of-interest algorithm. To demonstrate the capabilities of AriumMS, five datasets were combined. This includes three newly developed capillary electrophoresis (CE)-Orbitrap MS methods using the recently introduced nanoCEasy CE-MS interface and two hydrophilic interaction liquid chromatography (HILIC)-Orbitrap MS methods. AriumMS provides a novel mid-level data fusion approach for multi-platform data analysis to simplify and speed up multi-platform data processing and evaluation. The key feature of AriumMS lies in the optimized data processing strategy, including parallel processing of datasets and flexible parameterization for processing of individual separation methods with different peak characteristics. As a case study, Saccharomyces cerevisiae (yeast) was treated with a growth inhibitor, and AriumMS successfully differentiated the metabolome based on the augmented multi-platform CE-MS and HILIC-MS investigation. As a result, AriumMS is proposed as a powerful tool to improve the accuracy and selectivity of metabolome analysis through the integration of several HILIC-MS/CE-MS techniques.
    Keywords:  Augmented data evaluation; Capillary electrophoresis; Hydrophilic interaction liquid chromatography; Mid-level data fusion; Multi-platform metabolomics; nanoCEasy
  2. J Chromatogr A. 2023 May 18. pii: S0021-9673(23)00309-6. [Epub ahead of print]1702 464083
      Central carbon metabolism pathway (CCM) is one of the most important metabolic pathways in all living organisms and play crucial function in aspect of organism life. However, the simultaneous detection of CCM intermediates remains challenging. Here, we developed a chemical isotope labeling combined with LC-MS method for simultaneous determination of CCM intermediates with high coverage and accuracy. By chemical derivatization with 2-(diazo-methyl)-N-methyl-N-phenyl-benzamide (2-DMBA) and d5-2-DMBA, all CCM intermediates obtain better separation and accurate quantification at a single LC-MS run. The obtained limits of detection of CCM intermediates ranged from 5 to 36 pg/mL. Using this method, we achieved simultaneous and accurate quantification of 22 CCM intermediates in different biological samples. Take account of the high detection sensitivity of the developed method, this method was further applied to the quantification of CCM intermediates at single-cell level. Finally, 21 CCM intermediates were detected in 1000 HEK-293T cells and 9 CCM intermediates were detected in mouse kidney glomeruli optical slice samples (10∼100 cells).
    Keywords:  Central carbon metabolism; Chemical isotope labeling; LC−MS
  3. Anal Bioanal Chem. 2023 May 23.
      The present study systematically compares the sensitivity and selectivity of the analysis of multiple vitamin D metabolites after chemical derivatization using different reagents for liquid chromatography-tandem mass spectrometry (LC-MS/MS). Generally, chemical derivatization is applied to vitamin D metabolites to increase the ionization efficiency, which is particularly important for very low abundant metabolites. Derivatization can also improve the selectivity of the LC separation. A wide variety of derivatization reagents has been reported in recent years, but information on their relative performance and applicability to different vitamin D metabolites is, unfortunately, not available in the literature. To fill this gap, we investigated vitamin D3, 3β-25-hydroxyvitamin D3 (3β-25(OH)D3), 3α-25-hydroxyvitamin D3 (3α-25(OH)D3), 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), and 24,25-dihydroxyvitamin D3 (24,25(OH)2D3) and compared response factors and selectivity after derivatizing with several important reagents, including four dienophile reagents (4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), 4-[2-(6,7-dimethoxy-4-methyl-3-oxo-3,4-dihydroquinoxalinyl)ethyl]-1,2,4-triazoline-3,5-dione (DMEQ-TAD), Amplifex, 2-nitrosopyridine (PyrNO)) as well as two reagents targeting hydroxyl groups: isonicotinoyl chloride (INC) and 2-fluoro-1-methylpyridinium-p-toluenesulfonate (FMP-TS). In addition, a combination of dienophiles and hydroxyl group reagents was examined. For LC separations, reversed-phase C-18 and mixed-mode pentafluorophenyl HPLC columns using different compositions of the mobile phase were compared. With respect to detection sensitivity, the optimum derivatization reagent for the profiling of multiple metabolites was Amplifex. Nevertheless, FMP-TS, INC, PTAD, or PTAD combined with an acetylation reaction showed very good performance for selected metabolites. These reagent combinations provided signal enhancements on the order of 3- to 295-fold depending on the compound. Chromatographic separation of the dihydroxylated vitamin D3 species was readily achieved using any of the derivatization reactions, while for 25(OH)D3 epimers, only PyrNO, FMP, INC, and PTAD combined with acetylation enabled complete separation. In conclusion, we believe this study can serve as a useful reference for vitamin D laboratories, to help analytical and clinical scientists decide which derivatization reagent to choose for their application.
    Keywords:  25-Hydroxyvitamin D3; Chemical derivatization; Electrospray; Epimers; LC–MS/MS; Vitamin D3 metabolites
  4. J Agric Food Chem. 2023 May 26.
      Amino acids and acylcarnitines are important biomarkers of the body's energy state and can be used as diagnostic markers of certain inborn errors of metabolism. Few multianalyte methods for high-throughput analysis in serum exist for these compounds, but micromethods suitable for use in young children and infants are lacking. Therefore, we developed a quantitative high-throughput multianalyte hydrophilic interaction liquid chromatography-tandem mass spectrometry method preceded by a derivatization-free sample preparation using minimum amounts of serum (25 μL). Isotopically labeled standards were utilized for quantification. Forty amino acids and amino acid derivatives and 22 acylcarnitines were detected by applying a multiple reaction monitoring mode within a 20 min run. The method was comprehensively validated, comprising linearity, accuracy, (intraday/interday) precision, and quantitation limits, of which the latter ranged from 0.25 to 50 nM for acylcarnitines and from 0.005 to 1 μM for amino acids and their derivatives. Application of the method to 145 serum samples of three- to four-month-old healthy infants showed excellent reproducibility for multiday analyses and enabled simultaneous amino acid and acylcarnitine profiling in this age group.
    Keywords:  LC-MS; acylcarnitines; amino acids; infant; serum; stable isotope; underivatized
  5. Antioxidants (Basel). 2023 Apr 24. pii: 986. [Epub ahead of print]12(5):
      Thermal reactions can significantly alter the metabolomic and lipidomic content of biofluids and tissues during storage. In this study, we investigated the stability of polar metabolites and complex lipids in dry human serum and mouse liver extracts over a three-day period under various temperature conditions. Specifically, we tested temperatures of -80 °C (freezer), -24 °C (freezer), -0.5 °C (polystyrene box with gel-based ice packs), +5 °C (refrigerator), +23 °C (laboratory, room temperature), and +30 °C (thermostat) to simulate the time between sample extraction and analysis, shipping dry extracts to different labs as an alternative to dry ice, and document the impact of higher temperatures on sample integrity. The extracts were analyzed using five fast liquid chromatography-mass spectrometry (LC-MS) methods to screen polar metabolites and complex lipids, and over 600 metabolites were annotated in serum and liver extracts. We found that storing dry extracts at -24 °C and partially at -0.5 °C provided comparable results to -80 °C (reference condition). However, increasing the storage temperatures led to significant changes in oxidized triacylglycerols, phospholipids, and fatty acids within three days. Polar metabolites were mainly affected at storage temperatures of +23 °C and +30 °C.
    Keywords:  LC-MS; lipidomics; liquid chromatography; liver; mass spectrometry; metabolomics; oxidation; serum; shipping; stability; tissue
  6. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 May 18. pii: S1570-0232(23)00151-4. [Epub ahead of print]1225 123741
      High-intensity sweeteners ('sweeteners'), such as sucralose, saccharine, acesulfame, cyclamate and steviol, are replacing sugars in many food products, but biomarker-based data on their population-wide exposure, as well as analytical methods that can quantify urinary concentrations of sugars and sweeteners simultaneously, are lacking. Here, we developed and validated an ultra-pressure liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) method to quantify glucose, sucrose, fructose, sucralose, saccharine, acesulfame, cyclamate and steviol glucuronide in human urine. Urine samples were prepared by a simple dilution step containing the internal standards in water and methanol. Separation was achieved on a Shodex Asahipak NH2P-40 hydrophilic interaction liquid chromatography (HILIC) column using gradient elution. The analytes were detected using electrospray ionization in negative ion mode, and selective reaction monitoring was optimized using the [M-H]- ions. Calibration curves ranged between 34 and 19,230 ng/mL for glucose and fructose, and 1.8 to 1,026 ng/mL for sucrose and the sweeteners. The method has acceptable accuracy and precision, which depends on the application of appropriate internal standards. Storage of urine samples in lithium monophosphate gives the best overall analytical performance, and storage at room temperature without any preservatives should be avoided since this leads to reduced glucose and fructose concentrations. With the exception of fructose, all analytes were stable throughout 3 freeze-thaw cycles. The validated method was applied to human urine samples, demonstrating quantifiable concentrations of the analytes which were in the expected range. It is concluded that the method has acceptable performance to quantitatively determine dietary sugars and sweeteners in human urine.
    Keywords:  Biomarker; Fructose; Sucrose; Sweeteners; UPLC-MS/MS; Urine; Validation
  7. Anal Bioanal Chem. 2023 May 22.
      Identifying metabolites in model organisms is critical for many areas of biology, including unravelling disease aetiology or elucidating functions of putative enzymes. Even now, hundreds of predicted metabolic genes in Saccharomyces cerevisiae remain uncharacterized, indicating that our understanding of metabolism is far from complete even in well-characterized organisms. While untargeted high-resolution mass spectrometry (HRMS) enables the detection of thousands of features per analysis, many of these have a non-biological origin. Stable isotope labelling (SIL) approaches can serve as credentialing strategies to distinguish biologically relevant features from background signals, but implementing these experiments at large scale remains challenging. Here, we developed a SIL-based approach for high-throughput untargeted metabolomics in S. cerevisiae, including deep-48 well format-based cultivation and metabolite extraction, building on the peak annotation and verification engine (PAVE) tool. Aqueous and nonpolar extracts were analysed using HILIC and RP liquid chromatography, respectively, coupled to Orbitrap Q Exactive HF mass spectrometry. Of the approximately 37,000 total detected features, only 3-7% of the features were credentialed and used for data analysis with open-source software such as MS-DIAL, MetFrag, Shinyscreen, SIRIUS CSI:FingerID, and MetaboAnalyst, leading to the successful annotation of 198 metabolites using MS2 database matching. Comparable metabolic profiles were observed for wild-type and sdh1Δ yeast strains grown in deep-48 well plates versus the classical shake flask format, including the expected increase in intracellular succinate concentration in the sdh1Δ strain. The described approach enables high-throughput yeast cultivation and credentialing-based untargeted metabolomics, providing a means to efficiently perform molecular phenotypic screens and help complete metabolic networks.
    Keywords:  High-throughput sample generation; Liquid chromatography; Metabolomics; Saccharomyces cerevisiae; Stable isotope labelling; Untargeted high-resolution mass spectrometry
  8. Bioinform Adv. 2023 ;3(1): vbad061
      Motivation: Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used in metabolomics studies, while HILIC LC-MS is particularly suited for polar metabolites. Determining an optimized mobile phase and developing a proper liquid chromatography method tend to be laborious, time-consuming and empirical.Results: We developed a containerized web tool providing a workflow to quickly determine the optimized mobile phase by batch-evaluating chromatography peaks for metabolomics LC-MS studies. A mass chromatographic quality value, an asymmetric factor, and the local maximum intensity of the extracted ion chromatogram were calculated to determine the number of peaks and peak retention time. The optimal mobile phase can be quickly determined by selecting the mobile phase that produces the largest number of resolved peaks. Moreover, the workflow enables one to automatically process the repeats by evaluating chromatography peaks and determining the retention time of large standards. This workflow was validated with 20 chemical standards and successfully constructed a reference library of 571 metabolites for the HILIC LC-MS platform.
    Availability and implementation: MetaMOPE is freely available at Source code and installation instructions are available on GitHub:
    Supplementary information: Supplementary data are available at Bioinformatics Advances online.
  9. Metabolites. 2023 May 10. pii: 648. [Epub ahead of print]13(5):
      Untargeted and targeted approaches are the traditional metabolomics workflows acquired for a wider understanding of the metabolome under focus. Both approaches have their strengths and weaknesses. The untargeted, for example, is maximizing the detection and accurate identification of thousands of metabolites, while the targeted is maximizing the linear dynamic range and quantification sensitivity. These workflows, however, are acquired separately, so researchers compromise either a low-accuracy overview of total molecular changes (i.e., untargeted analysis) or a detailed yet blinkered snapshot of a selected group of metabolites (i.e., targeted analysis) by selecting one of the workflows over the other. In this review, we present a novel single injection simultaneous quantitation and discovery (SQUAD) metabolomics that combines targeted and untargeted workflows. It is used to identify and accurately quantify a targeted set of metabolites. It also allows data retro-mining to look for global metabolic changes that were not part of the original focus. This offers a way to strike the balance between targeted and untargeted approaches in one single experiment and address the two approaches' limitations. This simultaneous acquisition of hypothesis-led and discovery-led datasets allows scientists to gain more knowledge about biological systems in a single experiment.
    Keywords:  metabolomics; simultaneous quantitation and discovery (SQUAD); targeted metabolomics; untargeted metabolomics
  10. Anal Bioanal Chem. 2023 May 25.
      The balance between the different lipid molecules present in biological fluids accurately reflects the health state of the organism and can be used by medical personnel to finely tune therapy to a single patient, a process known as precision medicine. In this work, we developed a miniaturized workflow for the analysis of different lipid classes at the intact level, as well as their fatty acid constituents, starting from human serum. Fatty acids were identified by using flow-modulated comprehensive gas chromatography coupled to mass spectrometry (FM-GC × GC-MS), and their relative amount as well as the ratio of specific FA classes was determined by using FM-GC × GC with a flame ionization detector. Ultra-high-performance liquid chromatography coupled to tandem mass spectrometry was used for the simultaneous quantification of vitamin D metabolites and assessment of different intact lipid classes. An MRM method was developed for the quantification of five vitamin D metabolites (vitamin D2, vitamin D3, 25-hydroxyvitamin D2, 25-hydroxyvitamin D3, 24R,25-dihydroxyvitamin D3), and validated in terms of LoD, LoQ, accuracy, and precision, also using a certified reference material. At the same time, a combination of SCAN, precursor ion scan, and neutral loss scan, in both positive and negative modes, was used for the identification of 81 intact lipid species, such as phospholipids, cholesteryl esters, and triacylglycerols, in less than 25 min. In order to easily monitor the lipid composition and speed up the identification process, a two-dimensional map of the lipidome was generated, by plotting the molecular weight of the identified molecules versus their retention time. Moreover, a relative quantification was performed within each lipid class identified. The combination of untargeted and targeted data could provide useful information about the pathophysiological condition of the organism and evaluate, in a tailored manner, an efficient action.
    Keywords:  Comprehensive two-dimensional gas chromatography; Fatty acids; Lipidomic; Precision medicine; UHPLC-MS/MS; Vitamin D
  11. Cell Mol Biol Lett. 2023 May 20. 28(1): 43
      BACKGROUND: Although metabolomics continues to expand in many domains of research, methodological issues such as sample type, extraction and analytical protocols have not been standardized, impeding proper comparison between studies and future research.METHODS: In the present study, five solvent-based and solid-phase extraction methods were investigated in both plasma and serum. All these extracts were analyzed using four liquid chromatography coupled with high resolution mass spectrometry (LC-MS) protocols, either in reversed or normal-phase and with both types of ionization. The performances of each method were compared according to putative metabolite coverage, method repeatability and also extraction parameters such as overlap, linearity and matrix effect; in both untargeted (global) and targeted approaches using fifty standard spiked analytes.
    RESULTS: Our results verified the broad specificity and outstanding accuracy of solvent precipitation, namely methanol and methanol/acetonitrile. We also reveal high orthogonality between methanol-based methods and SPE, providing the possibility of increased metabolome coverage, however we highlight that such potential benefits must be weighed against time constrains, sample consumption and the risk of low reproducibility of SPE method. Furthermore, we highlighted the careful consideration about matrix choice. Plasma showed the most suitable in this metabolomics approach combined with methanol-based methods.
    CONCLUSIONS: Our work proposes to facilitate rational design of protocols towards standardization of these approaches to improve the impact of metabolomics research.
    Keywords:  Extraction; Guideline; Metabolomic; Methods; Suitability
  12. Anal Chem. 2023 May 23.
      Small molecule structure elucidation using tandem mass spectrometry (MS/MS) plays a crucial role in life science, bioanalytical, and pharmaceutical research. There is a pressing need for increased throughput of compound identification and transformation of historical data into information-rich spectral databases. Meanwhile, molecular networking, a recent bioinformatic framework, provides global displays and system-level understanding of complex LC-MS/MS data sets. Herein we present meRgeION, a multifunctional, modular, and flexible R-based toolbox to streamline spectral database building, automated structural elucidation, and molecular networking. The toolbox offers diverse tuning parameters and the possibility to combine various algorithms in the same pipeline. As an open-source R package, meRgeION is ideally suited for building spectral databases and molecular networks from privacy-sensitive and preliminary data. Using meRgeION, we have created an integrated spectral database covering diverse pharmaceutical compounds that was successfully applied to annotate drug-related metabolites from a published nontargeted metabolomics data set as well as reveal the chemical space behind this complex data set through molecular networking. Moreover, the meRgeION-based processing workflow has demonstrated the usefulness of a spectral library search and molecular networking for pharmaceutical forced degradation studies. meRgeION is freely available at:
  13. Anal Chim Acta. 2023 Jul 18. pii: S0003-2670(23)00495-6. [Epub ahead of print]1265 341274
      Lipidomics studies strive for a comprehensive identification and quantification of lipids. While reversed phase (RP) liquid chromatography (LC) coupled to high resolution mass spectrometry (MS) offers unrivalled selectivity and thus is the preferred method for lipid identification, accurate lipid quantification remains challenging. The widely adopted one-point lipid class specific quantification (one internal standard per lipid class) suffers from the fact that ionization of internal standard and target lipid occurs under different solvent composition as a consequence of chromatographic separation. To address this issue, we established a dual flow injection and chromatography setup that allows to control solvent conditions during ionization enabling isocratic ionization while running a RP gradient through the use of a counter-gradient. Using this dual LC pump platform, we investigated the impact of solvent conditions within a RP gradient on ionization response and arising quantification biases. Our results confirmed that changing solvent composition significantly influences ionization response. Quantification of human plasma (SRM 1950) lipids under gradient and isocratic ionization conditions further confirmed these findings as significant differences between the two conditions were found for the majority of lipids. While the quantity of sphingomyelins with >40 C atoms was consistently overestimated under gradient ionization, isocratic ionization improved their recovery compared to consensus values. However, the limitation of consensus values was demonstrated as overall only small changes in z-score were observed because of high uncertainties of the consensus values. Furthermore, we observed a trueness bias between gradient and isocratic ionization when quantifying a panel of lipid species standards which is highly dependent on lipid class and ionization mode. Uncertainty calculations under consideration of the trueness bias as RP gradient uncertainty revealed that especially ceramides with >40 C atoms had a high bias leading to total combined uncertainties of up to 54%. The assumption of isocratic ionization significantly decreases total measurement uncertainty and highlights the importance of studying the trueness bias introduced by a RP gradient to reduce quantification uncertainty.
    Keywords:  Human plasma; Ionization response; Lipidomics; Mass spectrometry; Quantification; Reversed-phase liquid chromatography
  14. Anal Chem. 2023 May 23.
      Electrospray ionization mass spectrometry (ESI-MS) is an established method for the identification of biomarkers. By nano-ESI (nESI), the polar molecular fraction of complex biological samples can be successfully ionized. In contrast, the less-polar free cholesterol, which serves as an important biomarker for several human diseases, is barely accessible by nESI. Although, complex scan functions of modern high-resolution MS devices are able to increase the signal-to-noise ratio, they are limited by the ionization efficiency of the nESI. One possible method to increase the ionization efficiency is the derivatization with acetyl chloride, however interferences with cholesteryl esters must be considered, so chromatographic separation or complex scan functions may be required. A novel approach to increase the yield of cholesterol ions of the nESI could be the application of a second consecutive-ionization process. This publication presents the flexible microtube plasma (FμTP) as a consecutive-ionization source, which allows the determination of cholesterol in nESI-MS analysis. Focusing on the analytical performance, the nESI-FμTP approach increases the cholesterol signal yield in a complex liver extract by a factor of 49. The repeatability and long-term stability could be successfully evaluated. A linear dynamic range of 1.7 orders of magnitude, a minimum detectability of 5.46 mg/L, and a high accuracy (deviation, -8.1%) demonstrates the nESI-FμTP-MS as an excellent approach for a derivatization-free determination of cholesterol.
  15. J Food Drug Anal. 2023 Mar 15. 31(1): 137-151
      New psychoactive substances (NPS) have been rapidly emerged as legal alternatives to controlled drugs, which raised severe public health issue. The detection and monitoring of its intake by complete metabolic profiling is an urgent and vital task. Untargeted metabolomics approach has been applied for several NPS metabolites studies. Although the number of such works is relatively limited but with a rapidly growing need. The present study aimed to propose a procedure that includes liquid chromatography high-resolution mass spectrometry (LC-HRMS) analysis and a signal selection software, MetaboFinder, programed as a web tool. The comprehensive metabolites profile of one kind of NPS, 4-methoxy-α-pyrrolidinovalerophenone (4-MeO-α-PVP), was studied by using this workflow. In this study, two different concentrations of 4-MeO-α-PVP along with as blank sample were incubated with human liver S9 fraction for the conversion to their metabolites and followed by LC-MS analysis. After retention time alignment and feature identification, 4640 features were obtained and submitted to statistical analysis for signal selection by using MetaboFinder. A total of 50 features were considered as 4-MeO-α-PVP metabolite candidates showing significant changes (p < 0.00001 and fold change >2) between the two investigated groups. Targeted LC-MS/MS analysis was conducted focusing on these significantly expressed features. Assisted by chemical formula determination according to high mass accuracy and in silico MS2 fragmentation prediction, 19 chemical structure identifications were achieved. Among which, 8 metabolites have been reported derived from 4-MeO-α-PVP in a previous literature while 11 novel 4-MeO-α-PVP metabolites were identified by using our strategy. Further in vivo animal experiment confirmed that 18 compounds were 4-MeO-α-PVP metabolites, which demonstrated the feasibility of our strategy for screening the 4-MeO-α-PVP metabolites. We anticipate that this procedure may support and facilitate traditional metabolism studies and potentially being applied for routine NPS metabolites screening.
  16. J Pharm Biomed Anal. 2023 May 05. pii: S0731-7085(23)00212-1. [Epub ahead of print]233 115443
      The emergence of new psychoactive substances currently exceeding a thousand is rapidly changing substance prevalence patterns and straining the methods used for detection, most of which are suitable only for a single class of substances. This study presents a rapid and facile dilute-and-shoot system operated in conjunction with an optimized liquid chromatographic separation system for the high-sensitivity detection of substances across a range of substance classes with 3 isotopes used only. The proposed method based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) is able to identify 68 substance and their metabolites in urine samples as small as 50 μL. Optimal chromatographic conditions including 95% water/methanol ratio with 0.1% added formic acid and a prolonged LC gradient run-time (15 min) improved the peak shape of polar compounds and enhanced signal strength by 5%. Under 4-fold dilution, all analytes were within 80-120% of tolerance response levels, indicating that the matrix effect was insignificant. In experiments, the limit of detection (LOD) ranged from 0.05 to 0.5 ng mL-1, while the coefficient of determination (R2) was > 0.9950. The retention time shift of each peak remained at < 2% with an inter-day relative standard deviation (RSD) of 0.9-14.9% and intra-day RSD of 1.1%- 13.8%. The rapid dilute-and-shoot presents a high-sensitivity, significant stability, robustness and reproducibility without serious interference. To demonstrate the effectiveness of the system, 532 urine samples were collected from suspected drug abusers, and the proposed method was used for rapid analysis. Of these samples, 79.5% contained between one and twelve analytes, and 12.4% tested positive for new psychoactive substances, mostly derivatives of amphetamine and synthetic cathinones. The study presents a high-sensitivity analytic system that is capable of detecting substances from multiple classes and can be used for effective monitoring of substance prevalence in urine.
    Keywords:  Dilute-and-shoot; Liquid chromatography-mass spectrometry; Multi-class psychoactive substances; Solid phase extraction; Urine
  17. J Mass Spectrom Adv Clin Lab. 2023 Aug;29 2-8
      Introduction: Tyrosine kinase inhibitors (TKIs) are widely used in tumor treatment. The detection of these medicines by liquid chromatography-tandem mass spectrometry (LC-MS/MS) can avoid the interference of structurally similar compounds.Objectives: This study aimed to develop and validate a new LC-MS/MS assay for the quantification of eight tyrosine kinase inhibitors in human plasma and to preliminarily evaluate the clinical utility of the therapeutic drug monitoring method.
    Methods: Plasma samples were prepared by simple protein precipitation and separated using an ultra-high-performance reversed phase column. Detection was achieved using a triple quadrupole mass spectrometer in the positive ionization mode. The assay was validated against standard guidelines. We reviewed and analyzed the results of 268 plasma samples obtained from patients administered imatinib and other TKIs collected from January 2020 to November 2021 at Zhongshan Hospital. The analytes were separated and quantified within 3.5 min.
    Results: The newly developed method demonstrated linearity for the detected drug concentration in the range of 20 to 2000 ng/ml for gefitinib (r2 = 0.991) and crizotinib (r2 = 0.992), 50 to 5000 ng/ml for nilotinib (r2 = 0.991) and imatinib (r2 = 0.995), 1500-150,000 ng/ml for vemurafenib (r2 = 0.998), 1000-100,000 ng/ml for pazopanib (r2 = 0.993), 0.5-100 ng/ml for axitinib (r2 = 0.992) and 5-500 ng/ml for sunitinib (r2 = 0.991) and N-desethyl sunitinib (r2 = 0.998). The lower limit of quantification (LLOQ) was 20 ng/ml for gefitinib and crizotinib, 50 ng/ml for nilotinib and imatinib, 1500 ng/ml for vemurafenib, 1000 ng/ml for pazopanib, 0.5, and 5 ng/ml for sunitinib and N-desethyl sunitinib, respectively. Specificity, precision, accuracy, and stability were tested, and met the requirements of the guidelines. At the same dose, there was no significant difference in plasma drug concentration between the original imatinib medicine and the generic medicine after patent expiration.
    Conclusion: We developed a sensitive and reliable method for the quantification of eight TKIs.
    Keywords:  Clinical application; Liquid chromatography-tandem mass spectrometry; Therapeutic drug monitoring; Tyrosine kinase inhibitors
  18. Metabolites. 2023 May 16. pii: 665. [Epub ahead of print]13(5):
      Untargeted metabolomics is an important tool in studying health and disease and is employed in fields such as biomarker discovery and drug development, as well as precision medicine. Although significant technical advances were made in the field of mass-spectrometry driven metabolomics, instrumental drifts, such as fluctuations in retention time and signal intensity, remain a challenge, particularly in large untargeted metabolomics studies. Therefore, it is crucial to consider these variations during data processing to ensure high-quality data. Here, we will provide recommendations for an optimal data processing workflow using intrastudy quality control (QC) samples that identifies errors resulting from instrumental drifts, such as shifts in retention time and metabolite intensities. Furthermore, we provide an in-depth comparison of the performance of three popular batch-effect correction methods of different complexity. By using different evaluation metrics based on QC samples and a machine learning approach based on biological samples, the performance of the batch-effect correction methods were evaluated. Here, the method TIGER demonstrated the overall best performance by reducing the relative standard deviation of the QCs and dispersion-ratio the most, as well as demonstrating the highest area under the receiver operating characteristic with three different probabilistic classifiers (Logistic regression, Random Forest, and Support Vector Machine). In summary, our recommendations will help to generate high-quality data that are suitable for further downstream processing, leading to more accurate and meaningful insights into the underlying biological processes.
    Keywords:  analytical variation; batch effects; metabolomics; quality control
  19. Chem Sci. 2023 May 24. 14(20): 5291-5301
      Sulfur is an essential element of life. Thiol-containing metabolites in all organisms are involved in the regulation of diverse biological processes. Especially, the microbiome produces bioactive metabolites or biological intermediates of this compound class. The analysis of thiol-containing metabolites is challenging due to the lack of specific tools, making these compounds difficult to investigate selectively. We have now developed a new methodology comprising bicyclobutane for chemoselective and irreversible capturing of this metabolite class. We utilized this new chemical biology tool immobilized onto magnetic beads for the investigation of human plasma, fecal samples, and bacterial cultures. Our mass spectrometric investigation detected a broad range of human, dietary and bacterial thiol-containing metabolites and we even captured the reactive sulfur species cysteine persulfide in both fecal and bacterial samples. The described comprehensive methodology represents a new mass spectrometric strategy for the discovery of bioactive thiol-containing metabolites in humans and the microbiome.
  20. Anal Chem. 2023 May 23.
      In recent years, feces has surfaced as the matrix of choice for investigating the gut microbiome-health axis because of its non-invasive sampling and the unique reflection it offers of an individual's lifestyle. In cohort studies where the number of samples required is large, but availability is scarce, a clear need exists for high-throughput analyses. Such analyses should combine a wide physicochemical range of molecules with a minimal amount of sample and resources and downstream data processing workflows that are as automated and time efficient as possible. We present a dual fecal extraction and ultra high performance liquid chromatography-high resolution-quadrupole-orbitrap-mass spectrometry (UHPLC-HR-Q-Orbitrap-MS)-based workflow that enables widely targeted and untargeted metabolome and lipidome analysis. A total of 836 in-house standards were analyzed, of which 360 metabolites and 132 lipids were consequently detected in feces. Their targeted profiling was validated successfully with respect to repeatability (78% CV < 20%), reproducibility (82% CV < 20%), and linearity (81% R2 > 0.9), while also enabling holistic untargeted fingerprinting (15,319 features, CV < 30%). To automate targeted processing, we optimized an R-based targeted peak extraction (TaPEx) algorithm relying on a database comprising retention time and mass-to-charge ratio (360 metabolites and 132 lipids), with batch-specific quality control curation. The latter was benchmarked toward vendor-specific targeted and untargeted software and our isotopologue parameter optimization/XCMS-based untargeted pipeline in LifeLines Deep cohort samples (n = 97). TaPEx clearly outperformed the untargeted approaches (81.3 vs 56.7-66.0% compounds detected). Finally, our novel dual fecal metabolomics-lipidomics-TaPEx method was successfully applied to Flemish Gut Flora Project cohort (n = 292) samples, leading to a sample-to-result time reduction of 60%.
  21. Anal Bioanal Chem. 2023 May 24.
      Mass spectrometry imaging (MSI) is an analytical technique that can detect and visualize thousands of m/z values resolved in two- and three-dimensional space. These m/z values lead to hundreds of molecular annotations, including on-tissue and background ions. Discrimination of sample-related analytes from ambient ions conventionally involves manual investigation of each ion heatmap, which requires significant researcher time and effort (for a single tissue image, it can take an hour to determine on-tissue and off-tissue species). Moreover, manual investigation lends itself to subjectivity. Herein, we present the utility of an ion classification tool (ICT) developed using object-based image analysis in MATLAB. The ICT functions by segmenting ion heatmap images into on-tissue and off-tissue objects through binary conversion. The binary images are analyzed and within seconds used to classify the ions as on-tissue or background using a binning approach based on the number of detected objects. In a representative dataset with 50 randomly selected annotations, the ICT was able to accurately classify 45/50 ions as on-tissue or background.
    Keywords:  IR-MALDESI; Image classification; Image segmentation; MATLAB; Mass spectrometry imaging; Object-based image analysis
  22. Metabolites. 2023 May 19. pii: 669. [Epub ahead of print]13(5):
      Mass spectrometry imaging (MSI) has been a key driver of groundbreaking discoveries in a number of fields since its inception more than 50 years ago. Recently, MSI development trends have shifted towards ambient MSI (AMSI) as the removal of sample-preparation steps and the possibility of analysing biological specimens in their natural state have drawn the attention of multiple groups across the world. Nevertheless, the lack of spatial resolution has been cited as one of the main limitations of AMSI. While significant research effort has presented hardware solutions for improving the resolution, software solutions are often overlooked, although they can usually be applied in a cost-effective manner after image acquisition. In this vein, we present two computational methods that we have developed to directly enhance the image resolution post-acquisition. Robust and quantitative resolution improvement is demonstrated for 12 cases of openly accessible datasets across laboratories around the globe. Using the same universally applicable Fourier imaging model, we discuss the possibility of true super-resolution by software for future studies.
    Keywords:  ambient mass spectrometry imaging; image restoration; single-image super-resolution
  23. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 May 06. pii: S1570-0232(23)00147-2. [Epub ahead of print]1225 123737
      Phytosterols are essential structural components of plant cell membranes and possess health-related benefits, including lowering blood cholesterol levels in humans. Numerous analytical methods are being used to profile plant and animal sterols. Chromatography hyphenated to tandem mass spectrometry, is a better option due to its specificity, selectivity, and sensitivity. An ultra-performance supercritical fluid chromatography hyphenated with atmospheric pressure chemical ionization (APCI) tandem mass spectrometric method was developed and evaluated for fingerprint analysis of seven phytosterols. Mass spectrometry fragmentation behavior was used for phytosterol identification, and multiple reaction monitoring scanning was utilized for phytosterol confirmation, where APCI outperformed superiority in terms of ion intensity, particularly in the production of [M + H-H2O]+ ions rather than [M + H]+ ions. The chromatographic conditions were thoroughly evaluated, and the ionization parameters were optimized as well. In a 3 min. run, the seven phytosterols were separated concurrently. The calibration and repeatability tests were conducted to check the instrument's performance, and the results indicated that all of the phytosterols tested had correlation coefficients (r2) greater than 0.9911 over the concentration range of 5-5000 ng/mL. The limit of quantification was below 20 ng/mL for all the tested analytes except for stigmasterol and campesterol. The partially validated method was applied for the evaluation of phytosterols in pure coconut oil and palm oil in order to demonstrate its applicability. Total sterols in coconut and palm oils were 126.77 ng/mL and 101.73 ng/mL, respectively. In comparison to earlier methods of phytosterol analysis, the novel method offers a far faster, more sensitive, and more selective analytical process.
    Keywords:  APCI; Atmospheric pressure chemical ionization; Coconut oil; Palm oil; Phytosterols; Supercritical fluid chromatography; Tandem mass spectrometry
  24. Anal Chem. 2023 May 22.
      The importance of element-selective detection with inductively coupled plasma mass spectrometry (ICPMS) has been significantly increased in recent years following the introduction of tandem ICPMS (ICPMS/MS), which unlocked access to nonmetal speciation analysis. However, nonmetals are ubiquitous, and the feasibility of nonmetal speciation analysis in matrices with complex metabolomes is yet to be demonstrated. Herein, we report the first phosphorous speciation study by HPLC-ICPMS/MS in a human sample, namely, urine, involving the determination of the natural metabolite and biomarker phosphoethanolamine. A simple one-step derivatization procedure was employed to enable the separation of the target compound from the hydrophilic phosphorous metabolome in urine. The challenge of eluting the hydrophobic derivative under ICPMS-compatible chromatographic conditions was addressed by employing hexanediol, a novel chromatographic eluent recently described in our previous work but has not yet been exploited in a real-world application. The developed method features fast chromatographic separation (<5 min), no need for an isotopically labeled internal standard, and an instrumental LOD of 0.5 μg P L-1. The method was evaluated for recovery (90-110%), repeatability (RSD ±5%), and linearity (r2 = 0.9998). The method accuracy was thoroughly examined by comparing with an independently developed method based on HPLC-ESIMS/MS without derivatization, where agreement was found within ±5-20%. An application is presented to gain first insight into the variability in the human excretion of phosphoethanolamine, which is key for the interpretation of its levels as a biomarker, by repeated urine collection from a group of volunteers over 4 weeks.
  25. Mol Cell Proteomics. 2023 May 18. pii: S1535-9476(23)00087-7. [Epub ahead of print] 100576
      Imaging Mass Spectrometry (IMS) is a molecular technology utilized for spatially driven research, providing molecular maps from tissue sections. This article reviews matrix-assisted laser desorption/ionization (MALDI) IMS and its progress as a primary tool in the clinical laboratory. MALDI MS has been used to classify bacteria and perform other bulk analyses for plate-based assays for many years. However, the clinical application of spatial data within a tissue biopsy for diagnoses and prognoses is still an emerging opportunity in molecular diagnostics. This work considers spatially driven mass spectrometry approaches for clinical diagnostics and addresses aspects of new imaging-based assays that include analyte selection, quality control/assurance metrics, data reproducibility, data classification, and data scoring. It is necessary to implement these tasks for the rigorous translation of IMS to the clinical laboratory; however, this requires detailed standardized protocols for introducing IMS into the clinical laboratory to deliver reliable and reproducible results that inform and guide patient care.
  26. Adv Food Nutr Res. 2023 ;pii: S1043-4526(22)00082-1. [Epub ahead of print]104 1-42
      Lipidomics is an emerging and promising omics derived from metabolomics to comprehensively analyze all of lipid molecules in biological matrices. The purpose of this chapter is to introduce the development and application of lipidomics for food research. First, three aspects of sample preparation are introduced: food sampling, lipid extraction, and transportation and storage. Second, five types of instruments for data acquisition are summarized: direct infusion-mass spectrometry (MS), chromatographic separation-MS, ion mobility-MS, MS imaging, and nuclear magnetic resonance spectroscopy. Third, data acquisition and analysis software are described for the lipidomics software development. Fourth, the application of lipidomics for food research is discussed such as food origin and adulteration analysis, food processing research, food preservation research, and food nutrition and health research. All the contents suggest that lipidomics is a powerful tool for food research based on its ability of lipid component profile analysis.
    Keywords:  Food research; Instrument development; Lipidomics; Lipids; Sample preparation; Software
  27. Metabolites. 2023 Apr 24. pii: 588. [Epub ahead of print]13(5):
      Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from archaeological human dentin. Dentin obtained from micro sampling the dental pulp of teeth of victims and non-victims of Yersinia pestis (plague) from a 6th century Cambridgeshire site are used to evaluate the potential use of such unique material for untargeted metabolomic studies on disease state through liquid chromatography hyphenated to high-resolution mass spectrometry (LC-HRMS). Results show that small molecules of both likely endogenous and exogenous sources are preserved for a range of polar and less polar/apolar metabolites in archaeological dentin; however, untargeted metabolomic profiles show no clear differentiation between healthy and infected individuals in the small sample analysed (n = 20). This study discusses the potential of dentin as a source of small molecules for metabolomic assays and highlights: (1) the need for follow up research to optimise sampling protocols, (2) the requirements of studies with larger sample numbers and (3) the necessity of more databases to amplify the positive results achievable with this Omic technique in the archaeological sciences.
    Keywords:  LC-HRMS; ancient metabolomics; biomolecular archaeology; disease; human dentin; plague; untargeted metabolomics
  28. Curr Opin Chem Biol. 2023 May 22. pii: S1367-5931(23)00065-0. [Epub ahead of print]75 102327
      Single cell metabolomics is a rapidly advancing field of bio-analytical chemistry which aims to observe cellular biology with the greatest detail possible. Mass spectrometry imaging and selective cell sampling (e.g. using nanocapillaries) are two common approaches within the field. Recent achievements such as observation of cell-cell interactions, lipids determining cell states and rapid phenotypic identification demonstrate the efficacy of these approaches and the momentum of the field. However, single cell metabolomics can only continue with the same impetus if the universal challenges to the field are met, such as the lack of strategies for standardisation and quantification, and lack of specificity/sensitivity. Mass spectrometry imaging and selective cell sampling come with unique advantages and challenges which, in many cases are complementary to each other. We propose here that the challenges specific to each approach could be ameliorated with collaboration between the two communities driving these approaches.
    Keywords:  Lipidomics; Mass spectrometry; Mass spectrometry imaging; Selective cell sampling; Single cell metabolomics
  29. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 May 13. pii: S1570-0232(23)00152-6. [Epub ahead of print]1225 123742
      Alterations in reduced and oxidized glutathione (GSH/GSSG) levels represent an important marker for oxidative stress and potential disease progression in toxicological research. Since GSH can be oxidized rapidly, using a stable and reliable method for sample preparation and GSH/GSSG quantification is essential to obtain reproducible data. Here we describe an optimised sample processing combined with a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, validated for different biological matrices (lysates from HepG2 cells, C. elegans, and mouse liver tissue). To avoid autoxidation of GSH, samples were treated with the thiol-masking agent N-ethylmaleimide (NEM) and sulfosalicylic acid (SSA) in a single step. With an analysis time of 5 min, the developed LC-MS/MS method offers simultaneous determination of GSH and GSSG at high sample throughput with high sensitivity. This is especially interesting with respect of screening for oxidative and protective properties of substances in in vitro and in vivo models, e.g. C. elegans. In addition to method validation parameters (linearity, limit of detection (LOD), limit of quantification (LOQ), recovery, interday, intraday), we verified the method by using menadione and L-buthionine-(S,R)-sulfoximine (BSO) as well established modulators of cellular GSH and GSSG concentrations. Thereby menadione proved to be a reliable positive control also in C. elegans.
    Keywords:  Biological matrices; Glutathione; Glutathione disulfide; LC-MS/MS
  30. Pharmaceutics. 2023 May 18. pii: 1524. [Epub ahead of print]15(5):
      Poly (ADP-ribose) polymerase inhibitors (PARPis) are becoming increasingly meaningful in oncology, and their therapeutic drug monitoring (TDM) might be beneficial for patients. Several bioanalytical methods have been reported for PARPis quantification in human plasma, but advantages might be obtained using dried blood spot (DBS) as a sampling technique. Our aim was to develop and validate a liquid chromatography-tandem mass spectrometric (LC-MS/MS) method for olaparib, rucaparib, and niraparib quantification in both human plasma and DBS matrices. Additionally, we aimed to assess the correlation between the drug concentrations measured in these two matrices. DBS from patients was obtained using Hemaxis DB10 for volumetric sampling. Analytes were separated on a Cortecs-T3 column and detected with electrospray ionization (ESI)-MS in positive ionization mode. Validation was performed according to the latest regulatory guidelines, in the range (ng/mL) 140-7000 for olaparib, 100-5000 for rucaparib, and 60-3000 for niraparib, within the hematocrit (Hct) range 29-45%. The Passing-Bablok and Bland-Altman statistical analyses revealed a strong correlation between plasma and DBS for olaparib and niraparib. However, due to the limited amount of data, it was challenging to establish a robust regression analysis for rucaparib. To ensure a more reliable assessment, additional samples are required. The DBS-to-plasma ratio was used as a conversion factor (CF) without considering any patient-related hematological parameters. These results provide a solid basis for the feasibility of PARPis TDM using both plasma and DBS matrices.
    Keywords:  LC-MS/MS; PARP inhibitors; dried blood spot; human plasma; niraparib; olaparib; rucaparib; therapeutic drug monitoring
  31. J Agric Food Chem. 2023 May 25.
      Recent studies show the immense capacities of the unified quantitation of aroma and taste compounds using liquid chromatography-mass spectrometry (LC-MS). The goal of this study was to highlight the broad application of this unified method. Thus, a stable isotope dilution analysis quantification method of the most important key food odorants in various food categories by LC-MS was developed. Using the well-known derivatization agent 3-nitrophenylhydrazine for carbonyl derivatization and a newly developed approach for alcohol and thiol derivatization, a method for the quantitation of 20 key food odorants was established. Intraday precision was determined to be ≤26%, and interday precision was between 24 and 31%. Limits of quantitation were determined between 0.014 and 283 μg/kg. The work shows that a wide array of aroma compounds can be analyzed accurately by LC-MS.
    Keywords:  3-nitrophenylhydrazine; LC−MS; aroma analysis; flavor analysis; generalists; stable isotope dilution assay