bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒07‒02
twenty-six papers selected by
Sofia Costa

  1. Anal Chim Acta. 2023 Sep 01. pii: S0003-2670(23)00688-8. [Epub ahead of print]1272 341467
      Liquid chromatography mass spectrometry (LC-MS) has been increasingly used for metabolome analysis. One of the critical steps in the LC-MS metabolome analysis workflow is related to metabolite identification. Among the measured parameters, peak mass is commonly used to search against a database for potential metabolite matches. Higher accuracy mass measurement allows the use of a narrower mass tolerance window for mass search. While various types of mass analyzers can routinely measure a peak mass with an error of less than a few ppm, mass measurement accuracy is not uniform for peaks with different intensities, particularly for quadrupole time-of-flight (QTOF) MS. Herein we present a simple and convenient method to determine the relation between peak intensity and mass error in LC-QTOF-MS-based metabolome analysis, followed by intensity-dependent mass search (IDMS) of a database for metabolite matches. This method is based on running a series of sodium formate mass calibrants, as part of the standard operating procedure (SOP) in LC-MS data acquisition, and then curve-fitting the measured mass errors and peak intensities. We show that, in two different quadrupole time-of-flight (QTOF) mass analyzers, mass accuracy is generally reduced as peak intensity decreases, which is independent of m/z values in the range commonly used for metabolite detection (e.g., m/z < 1000). We demonstrate the improvement in metabolite matches using IDMS in the analyses of dansyl labeled standards and human urine samples. We have implemented the IDMS method in the freely available MCID database at, which is composed of 8021 known human endogenous metabolites and their predicted metabolic products (375,809 compounds from one metabolic reaction and 10,583,901 compounds from two reactions).
    Keywords:  Chemical derivatization; Database search; Mass spectrometry; Metabolite identification; Metabolomics; QTOF
  2. J Am Soc Mass Spectrom. 2023 Jun 30.
      Anabolic steroids are of high biological interest due to their involvement in human development and disease progression. Additionally, they are banned in sport due to their performance-enhancing characteristics. Analytical challenges associated with their measurement stem from structural heterogeneity, poor ionization efficiency, and low natural abundance. Their importance in a variety of clinically relevant assays has prompted the consideration of integrating ion mobility spectrometry (IMS) into existing LC-MS assays, due primarily to its speed and structure-based separation capability. Herein we have optimized a rapid (2 min) targeted LC-IM-MS method for the detection and quantification of 40 anabolic steroids and their metabolites. First, a steroid-specific calibrant mixture was developed to cover the full range of retention time, mobility, and accurate mass. Importantly, this use of this calibrant mixture provided robust and reproducible measurements based on collision cross section (CCS) with interday reproducibility of <0.5%. Furthermore, the combined separation power of LC coupled to IM provided comprehensive differentiation of isomers/isobars within 6 different isobaric groups. Multiplexed IM acquisition also provided improved limits of detection, which were well below 1 ng/mL in almost all compounds measured. This method was also capable of steroid profiling, providing quantitative ratios (e.g., testosterone/epitestosterone, androsterone/etiocholanolone, etc.). Lastly, phase II steroid metabolites were probed in lieu of hydrolysis to demonstrate the ability to separate those analytes and provide information beyond total steroid concentration. This method has tremendous potential for rapid analysis of steroid profiles in human urine spanning a variety of applications from developmental disorders to doping in sport.
    Keywords:  Anabolic Steroids; Ion Mobility-Mass Spectrometry
  3. Bioinformatics. 2023 Jun 26. pii: btad406. [Epub ahead of print]
      MOTIVATION: Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) experiments aim to produce high quality fragmentation spectra which can be used to annotate metabolites. However, current Data-Dependent Acquisition (DDA) approaches may fail to collect spectra of sufficient quality and quantity for experimental outcomes, and extend poorly across multiple samples by failing to share information across samples or by requiring manual expert input.RESULTS: We present TopNEXt, a real-time scan prioritisation framework that improves data acquisition in multi-sample LC-MS/MS metabolomics experiments. TopNEXt extends traditional DDA exclusion methods across multiple samples by using a Region of Interest (RoI) and intensity-based scoring system. Through both simulated and lab experiments we show that methods incorporating these novel concepts acquire fragmentation spectra for an additional 10% of our set of target peaks and with an additional 20% of acquisition intensity. By increasing the quality and quantity of fragmentation spectra, TopNEXt can help improve metabolite identification with a potential impact across a variety of experimental contexts.
    AVAILABILITY: TopNEXt is implemented as part of the ViMMS framework and the latest version can be found at A stable version used to produce our results can be found at 10.5281/zenodo.7468914. Data can be found at 10.5525/gla.researchdata.1382.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  4. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 Jun 22. pii: S1570-0232(23)00209-X. [Epub ahead of print]1227 123799
      Recent scientific studies in the field of health and nutrition have unanimously affirmed the importance of consuming the omega-3 fatty acids, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), because of their cardioprotective properties. Fatty acid profiling in erythrocyte membranes allows the omega-3 index, which is a recognized indicator of the risk of developing cardiovascular disease, to be calculated. One consequence of the upward trend in healthy lifestyles and longevity is an increase in the number of studies into the omega-3 index, which requires a reliable method for the quantitative analysis of fatty acids. This article describes the development and validation of a sensitive and reproducible liquid chromatography tandem mass spectrometry (HPLC-MS/MS) method for the quantitative analysis of 23 fatty acids (in the form of fatty acid methyl esters, FAMEs) in 40 µl of whole blood and erythrocytes. The list of acids includes saturated, omega-9 unsaturated, omega-6 unsaturated and omega-3 unsaturated fatty acids as well as their trans-isomers. The limit of quantitation was 250 ng ml-1 for C12:0, C16:0 and C18:0; and 62.5 ng ml-1 for other FAMEs, including EPA, DHA and trans-isomers of FAME C16:1, C18:1 and C18:2 n-6. Sample preparation for fatty acid (FA) esterification/methylation with boron trifluoride-methanol (BF3) has been optimized. Chromatographic separation has been carried out on a C8 column in gradient mode using a mixture of acetonitrile, isopropanol and water with the addition of 0.1% formic acid and 5 mM ammonium formate. As a result, the problem of separating the cis- and trans-isomers of FAME C16:1, C18:1 and C18:2 n-6 has been solved. The electrospray ionization mass spectrometry (ESI-MS) detection of FAMEs, in the form of ammonium adducts, has been optimized for the first time, which has made the method more sensitive that when the protonated species are used. This method has been applied to 12 samples from healthy subjects that consumed omega-3 supplements and has proven to be a reliable tool for determining the omega-3 index.
    Keywords:  Ammonium adducts; FAMEs; Fatty acids; LC-MS/MS; Omega-3 index; PUFAs
  5. Exp Ther Med. 2023 Jul;26(1): 342
      With time, the number of samples in clinical laboratories from therapeutic drug monitoring has increased. Existing analytical methods for blood cyclosporin A (CSA) monitoring, such as high-performance liquid chromatography (HPLC) and immunoassays, have limitations including cross-reactivity, time consumption, and the complicated procedures involved. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has long been considered the reference standard owing to its high accuracy, specificity, and sensitivity. However, large numbers of blood samples, multi-step preparation procedures, and longer analytical times (2.5-20 min) are required as a consequence of the different technical strategies, to ensure good analytical performance and routine quality assurance. A stable, reliable, and high throughput detection method will save personnel time and reduce laboratory costs. Therefore, a high throughput and simple LC-MS/MS method was developed and validated for the detection of whole-blood CSA with CSA-d12 as the internal standard in the present study. Whole blood samples were prepared through a modified one-step protein precipitation method. A C18 column (50x2.1 mm, 2.7 µm) with a mobile phase flow rate of 0.5 ml/min was used for chromatographic separation with a total running time of 4.3 min to avoid the matrix effect. To protect the mass spectrometer, only part of the sample after LC separation was allowed to enter the mass spectrum, using two HPLC systems coupled to one mass spectrometry. In this way, throughput was improved with detection of two samples possible within 4.3 min using a shorter analytical time for each sample of 2.15 min. This modified LC-MS/MS method showed excellent analytical performance and demonstrated less matrix effect and a wide linear range. The design of multi-LC systems coupled with one mass spectrometry may play a notable role in the improvement of daily detection throughput, speeding up LC-MS/MS, and allowing it to be an integral part of continuous diagnostics in the near future.
    Keywords:  LC-MS/MS; clinical application; cyclosporin A; mass specimen; throughput
  6. Anal Chem. 2023 Jun 30.
      Glycosylation of metabolites serves multiple purposes. Adding sugars makes metabolites more water soluble and improves their biodistribution, stability, and detoxification. In plants, the increase in melting points enables storing otherwise volatile compounds that are released by hydrolysis when needed. Classically, glycosylated metabolites were identified by mass spectrometry (MS/MS) using [M-sugar] neutral losses. Herein, we studied 71 pairs of glycosides with their respective aglycones, including hexose, pentose, and glucuronide moieties. Using liquid chromatography (LC) coupled to electrospray ionization high-resolution mass spectrometry, we detected the classic [M-sugar] product ions for only 68% of glycosides. Instead, we found that most aglycone MS/MS product ions were conserved in the MS/MS spectra of their corresponding glycosides, even when no [M-sugar] neutral losses were observed. We added pentose and hexose units to the precursor masses of an MS/MS library of 3057 aglycones to enable rapid identification of glycosylated natural products with standard MS/MS search algorithms. When searching unknown compounds in untargeted LC-MS/MS metabolomics data of chocolate and tea, we structurally annotated 108 novel glycosides in standard MS-DIAL data processing. We uploaded this new in silico-glycosylated product MS/MS library to GitHub to enable users to detect natural product glycosides without authentic chemical standards.
  7. Brief Bioinform. 2023 Jun 27. pii: bbad244. [Epub ahead of print]
      Untargeted metabolomics is gaining widespread applications. The key aspects of the data analysis include modeling complex activities of the metabolic network, selecting metabolites associated with clinical outcome and finding critical metabolic pathways to reveal biological mechanisms. One of the key roadblocks in data analysis is not well-addressed, which is the problem of matching uncertainty between data features and known metabolites. Given the limitations of the experimental technology, the identities of data features cannot be directly revealed in the data. The predominant approach for mapping features to metabolites is to match the mass-to-charge ratio (m/z) of data features to those derived from theoretical values of known metabolites. The relationship between features and metabolites is not one-to-one since some metabolites share molecular composition, and various adduct ions can be derived from the same metabolite. This matching uncertainty causes unreliable metabolite selection and functional analysis results. Here we introduce an integrated deep learning framework for metabolomics data that take matching uncertainty into consideration. The model is devised with a gradual sparsification neural network based on the known metabolic network and the annotation relationship between features and metabolites. This architecture characterizes metabolomics data and reflects the modular structure of biological system. Three goals can be achieved simultaneously without requiring much complex inference and additional assumptions: (1) evaluate metabolite importance, (2) infer feature-metabolite matching likelihood and (3) select disease sub-networks. When applied to a COVID metabolomics dataset and an aging mouse brain dataset, our method found metabolic sub-networks that were easily interpretable.
    Keywords:  deep learning; feature selection; uncertainty matching; untargeted metabolomics
  8. Heliyon. 2023 Jun;9(6): e17230
      A sensitive, convenient, rapid and economic liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed to determine cinacalcet concentration in human plasma. A stable isotope cinacalcet (cinacalcet-D3) was selected as internal standard and the analytes were extracted from plasma samples by a one-step precipitation procedure. Chromatography separation was conducted on an Eclipse Plus C18 column by gradient elution with mobile phase of methanol-water-ammonium formate system at a constant flow rate of 0.6 mL/min. Mass spectrometric detection was conducted by multiple reaction monitoring using positive electrospray ionization. Cinacalcet concentrations in human plasma were determined over the concentration range of 0.1-50 ng/mL. The accuracies of lower limit of quantification (LLOQ) and quality control samples were all within the range of 85-115%, and the inter- and intra-batch precisions (CV%) were all within 15%. The average extraction recovery rates were 95.67-102.88%, and the quantification was not interfered by the matrix components. The validated method was successfully applied to determined cinacalcet concentrations in human plasma from secondary hyperparathyroidism patients.
    Keywords:  Cinacalcet; Human plasma; LC-MS/MS; One-step precipitation
  9. J Chromatogr A. 2023 Jun 16. pii: S0021-9673(23)00367-9. [Epub ahead of print]1705 464141
      In this work, a comprehensive method for the simultaneous determination of 33 diverse persistent and mobile organic compounds (PMOCs) in human urine was developed by dilute-and-shoot (DS) followed by mixed-mode liquid chromatography coupled with tandem mass spectrometry (MMLC-MS/MS). In the sample preparation step, DS was chosen since it allowed the quantification of all targets in comparison to lyophilization. For the chromatographic separation, Acclaim Trinity P1 and P2 trimodal columns provided greater capacity for retaining PMOCs than reverse phase and hydrophilic interaction liquid chromatography. Therefore, DS was validated at 5 and 50 ng/mL in urine with both mixed mode columns at pH = 3 and 7. Regarding figures of merit, linear calibration curves (r2 > 0.999) built between instrumental quantification limits (mostly below 5 ng/mL) and 500 ng/mL were achieved. Despite only 60% of the targets were recovered at 5 ng/mL because of the dilution, all PMOCs were quantified at 50 ng/mL. Using surrogate correction, apparent recoveries in the 70-130% range were obtained for 91% of the targets. To analyse human urine samples, the Acclaim Trinity P1 column at pH = 3 and 7 was selected as a consensus between analytical coverage (i.e. 94% of the targets) and chromatographic runs. In a pooled urine sample, industrial chemicals (acrylamide and bisphenol S), biocides and their metabolites (2-methyl-4-isothiazolin-3-one, dimethyl phosphate, 6-chloropyridine-3-carboxylic acid, and ammonium glufosinate) and an artificial sweetener (aspartame) were determined at ng/mL levels. The outcomes of this work showed that humans are also exposed to PMOCs due to their persistence and mobility, and therefore, further human risk assessment is needed.
    Keywords:  Dilute-and-shoot (DS); Human urine; Mixed-mode liquid chromatography (MMLC); Persistent and mobile organic compounds (PMOCs)
  10. Anal Sci. 2023 Jun 30.
      Boswellia serrata (B. serrata) is an important medicinal plant widely used as dietary supplements to provide a support for osteoarthritic and inflammatory diseases. The occurrence of triterpenes in leaves of B. serrata is very little or none. Therefore, the qualitative and quantitative determination of phytoconstituents (triterpenes and phenolics) present in the leaves of B. serrata is very much needed. The aim of this study was to develop an easy, rapid, efficient and simultaneous liquid chromatography-mass spectrometry (LC-MS/MS) method for the identification and quantification of the compounds present in the leaves extract of B. serrata. The purification of ethyl acetate extracts of B. serrata was performed by solid phase extraction method, followed by HPLC-ESI-MS/MS analysis. Chromatographic parameters of the analytical method included negative electrospray ionization (ESI-) with a flow of 0.5 mL/min in gradient mode consisting of acetonitrile (A) and water (B) containing 0.1% formic acid, at 20 °C. Total 19 compounds (13 triterpenes and 6 phenolic compounds) were separated, and simultaneously quantified using a validated LC-MS/MS method with high accuracy and sensitivity. Good linearity was obtained with r2 > 0.973 in the calibration range. The overall recoveries were in a range between 95.78 and 100.2% with relative standard deviations (RSD) below 5% for the entire procedure of matrix spiking experiments. Overall, there was no ion suppression from the matrix. The quantification data showed that the total amount of triterpenes and phenolic compounds in the leaves of B. serrata ethyl acetate extract samples ranged from 14.54 to 102.14 mg/g and 2.14 to 93.12 mg/g of dry extract, respectively. This work provides, for the first time, a chromatographic fingerprinting analysis on the leaves of B. serrata. A rapid, efficient, and simultaneous liquid chromatography-mass spectrometry (LC-MS/MS) method was developed and used for the both identification and quantification of triterpenes and phenolic compounds in the leaves extracts of B. serrata. The method established in this work can be used as quality-control method for other market formulations or dietary supplements containing leaf extract of B. serrata.
    Keywords:  Boswellia serrata; LC-ESI-MS/MS; Leaf extract; Phenolic compounds; Triterpenes
  11. Molecules. 2023 Jun 06. pii: 4580. [Epub ahead of print]28(12):
      Herein, we used isotopic formaldehyde and sodium cyanoborohydride via reductive amination to label two methyl groups on primary amine to arrange the standards (h2-formaldehyde-modified) and internal standards (ISs, d2-formaldehyde-modified) of tryptophan and its metabolites, such as serotonin (5-hydroxytryptamine) and 5-hydroxytryptophan. These derivatized reactions with a high yield are very satisfactory for manufacturing standards and ISs. This strategy will generate one or two methyl groups on amine to create different mass unit shifts with 14 vs. 16 or 28 vs. 32 in individual compounds for biomolecules with amine groups. In other words, multiples of two mass units shift are created using this derivatized method with isotopic formaldehyde. Serotonin, 5-hydroxytryptophan, and tryptophan were used as examples to demonstrate isotopic formaldehyde-generating standards and ISs. h2-formaldehyde-modified serotonin, 5-hydroxytryptophan, and tryptophan are standards to construct calibration curves, and d2-formaldehyde-modified analogs such as ISs spike into samples to normalize the signal of each detection. We utilized multiple reaction monitoring modes and triple quadrupole mass spectrometry to demonstrate the derivatized method suitable for these three nervous biomolecules. The derivatized method demonstrated a linearity range of the coefficient of determinations between 0.9938 to 0.9969. The limits of detection and quantification ranged from 1.39 to 15.36 ng/mL.
    Keywords:  5-hydroxytryptophan; multiple reaction monitoring; reductive amination; serotonin; tryptophan
  12. Se Pu. 2023 Jul;41(7): 632-639
      Kojic acid naturally appears in fermented foods and can be formed during the aerobic fermentation process induced by Aspergillus and Penicillium fungi. It is widely used in the food industry because it exhibits antibacterial and antifungal properties and does not affect food taste. However, recent studies indicate that kojic acid may be a potential carcinogen. Therefore, assessing the health risks of kojic acid in fermented foods are of great importance, and developing a sensitive and accurate analytical method for this compound is a significant endeavor. Much efforts have been devoted to the detection of kojic acid using electrochemistry, high performance liquid chromatography (HPLC), gas chromatography-mass spectrometry (GC-MS), and high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). HPLC and HPLC-MS/MS are the analytical techniques most often employed for this purpose. Of these two methods, HPLC-MS/MS displays excellent sensitivity and is the optimal selective technique. Pretreatment is usually necessary for kojic acid determination because of the complex matrix effects of fermented foods. However, few researches on the determination of kojic acid in food are available, and, to the best of our knowledge, the determination of kojic acid using solid-phase extraction (SPE) pretreatment has not been reported yet. Herein, a convenient, sensitive, and accurate method was developed to determine kojic acid in fermented foods using solid-phase extraction-ultra performance liquid chromatography-tandem mass spectrometry (SPE-UPLC-MS/MS). The pretreatment conditions, such as the extraction solvent, cartridge, rinse solvent, and eluent, were systematically optimized. The samples, including soy sauce, vinegar, liquor, sauce, fermented soya bean, and fermented bean curd, were extracted with 0.1% formic acid-absolute ethyl alcohol and purified using a PRiME HLB cartridge. Kojic acid was separated using an ACQUITY UPLC® BEH C18 column (100 mm×2.1 mm, 1.7 μm) with formic acid-acetonitrile (1∶999, v/v) and formic acid-5 mmol/L ammonium acetate (1∶999, v/v) solutions as the mobile phases under gradient elution mode. MS was performed in electrospray positive ionization (ESI+) and multiple reaction monitoring (MRM) modes. An internal standard method was used for quantification. Under optimized conditions, good linearity was achieved at mass concentrations of 5.0-100.0 μg/L, with a correlation coefficient (r) of 0.9994. The limits of detection and quantification of the method for kojic acid were 2-5 μg/kg and 6-15 μg/kg, respectively. Good recoveries of 86.8%-111.7%, intra-day precisions of 1.0%-7.9% (n=6), and inter-day precisions of 2.7%-10.2% (n=5) were also obtained. The matrix effect was evaluated by establishing a matrix-matching calibration curve, and weak inhibitory effects were found in vinegar and liquor; moderate inhibitory effects in fermented bean curd, fermented soya bean, and soy sauce; and a strong inhibitory effect in sauce. The developed method was used to detect kojic acid in 240 fermented foods, and the results showed that the detection rate of vinegar was the highest, followed by liquor, sauce, soy sauce, fermented soya bean, and fermented bean curd, the contents were 5.69-2272 μg/kg. Matrix interferences can be significantly reduced by optimizing the pretreatment and detection procedures. The proposed method is sensitive, accurate, and can be used to analyze kojic acid in fermented foods.
    Keywords:  fermented foods; kojic acid; solid-phase extraction (SPE); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  13. Talanta. 2023 Jun 22. pii: S0039-9140(23)00615-X. [Epub ahead of print]265 124864
      In this work, an analytical method based on solid-phase extraction (SPE) followed by liquid chromatography-tandem mass spectrometry analysis (LC-MS/MS) has been developed for the selective determination of thyroxine (T4) in human serum. For this purpose, two immunosorbents (ISs) specific to T4 were synthesized by grafting two different T4-specific monoclonal antibodies on a cyanogen bromide (CNBr)-activated-Sepharose® 4B solid support. The grafting yields obtained from the immobilization of each antibody on the CNBr-activated-Sepharose® 4B were over 90%, demonstrating that most of the antibodies were covalently bound to the solid support. The SPE procedure was optimized by studying the retention capability and selectivity of the two ISs in pure media fortified with T4. Under the optimized conditions, high elution efficiencies were achieved in the elution fraction for both specific ISs (i.e., 85%), whereas low ones were obtained in the control ISs (ca. 2%), showing the selectivity of the specific ISs. The ISs were also characterized by studying extraction and synthesis repeatability (RSD <8%), and capacity (104 ng of T4 per 35 mg of ISs, i.e., 3 μg g-1). Finally, the methodology was applied to a pooled human serum sample in order to study its analytical utility and accuracy. Relative recovery (RR) values between 81 and 107% were obtained, showing no matrix effects during the global methodology. Furthermore, the need to perform the immunoextraction was evidenced by comparing the LC-MS scan chromatograms and RR values with and without applying the immunoextraction procedure on a serum sample submitted to protein precipitation. This works exploits, for the first time, the use of an IS on the selective determination of T4 in human serum samples.
    Keywords:  Human serum; Immunosorbent; Liquid chromatography-tandem mass spectrometry; Solid-phase extraction; Thyroxine
  14. Talanta. 2023 Jun 20. pii: S0039-9140(23)00546-5. [Epub ahead of print]265 124795
      Lipids and metabolites are small biological molecules that act major roles in cellular functions. Multicellular tumor spheroids (MCTS) are a highly beneficial three-dimensional cellular model for cancer research due to their ability to imitate numerous characteristics of tumor tissues. Increasing studies have performed spatial lipidomics and metabolomics in MCTS using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). However, these approaches often lack the sensitivity and specificity to offer a comprehensive characterization of lipids and metabolites within MCTS. In this study, we addressed this challenge by utilizing MALDI combined with laser-induced postionization (MALDI-2) and trapped ion mobility spectrometry (TIMS) imaging in H295R adrenocortical MCTS. Our results showed that MALDI-2 could detect more lipids and metabolites in MCTS than the traditional MALDI. TIMS data revealed a successful separation of many isomeric and isobaric ions of lipids and metabolites with different locations (e.g., proliferative region and necrotic region) within MCTS, suggesting an enhanced peak capacity for spatial lipidomics and metabolomics. To further identify these isomeric and isobaric ions, we performed MS/MS imaging experiments to compare the differences in signal intensities and spatial distributions of product ions. Our data highlight the strong potential of MALDI-2 and TIMS imaging for analyzing lipids and metabolites in MCTS, which may serve as valuable tools for numerous fields of biological and medical research.
    Keywords:  MALDI combined with laser-induced postionization; Mass spectrometry imaging; Matrix-assisted laser desorption/ionization (MALDI); Multicellular tumor spheroids; Trapped ion mobility spectrometry
  15. Metabolites. 2023 Jun 15. pii: 755. [Epub ahead of print]13(6):
      A sensitive, selective and particularly fast method of liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed and validated for the determination of meloxicam and its main metabolite, 5'-carboxymeloxicam, in oral fluid samples. Meloxicam and its major metabolite were separated using a Shim-Pack XR-ODS 75 L × 2.0 column and C18 pre-column at 40 °C using a mixture of methanol and 10 mM ammonium acetate (80:20, v/v) with an injection flow rate of 0.3 mL/min. The total time of the analytical run was 5 min. Sixteen volunteers had oral fluid samples collected sequentially before and after taking a meloxicam tablet (15 mg) for up to 96 h. With the concentrations obtained, the pharmacokinetic parameters were determined using the Phoenix WinNonlin software. The parameters evaluated for meloxicam and 5'-carboxymeloxicam in the oral fluid samples showed linearity, accuracy, precision, medium-quality control (MQC-78.12 ng/mL), high-quality control (HQC-156.25 ng/mL), lower limits of quantification (LLOQ-0.6103 ng/mL), low-quality control (LQC-2.44 ng/mL), stability and dilution. Prostaglandin E2 (PGE2) was also detected and quantified in the oral fluid samples, demonstrating the possibility of a pharmacokinetic/pharmacodynamic (PK/PD) study with this methodology. All the parameters evaluated in the validation of the methodology in the oral fluid samples proved to be stable and within the possible variations in each of the described parameters. Through the data presented, the possibility of a PK/PD study was demonstrated, detecting and quantifying meloxicam, its main metabolite and PGE2 in oral fluid samples using LC-MS/MS.
    Keywords:  5′-carboxymeloxicam; mass spectrometry; meloxicam; oral fluid
  16. J AOAC Int. 2023 Jun 30. pii: qsad079. [Epub ahead of print]
      BACKGROUND: Taurine is recognized as an essential growth factor and as being critical in the maintenance of functional tissue regulation.OBJECTIVE: To evaluate the analytical performance of a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method for compliance with AOAC Standard Method Performance Requirements (SMPR®) for taurine analysis described in SMPR 2014.013.
    METHOD: Following protein precipitation with Carrez solutions, taurine is extracted and separated by HILIC with detection by triple quadrupole MS using multiple reaction monitoring. Stable isotope labelled taurine internal standard is used for quantification to correct for losses in extraction and variations in ionization in the ion source.
    RESULTS: The method was shown to meet the requirements specified in the SMPR with a linear range of 0.27-2700 mg/hg RTF (ready-to-feed), a limit of detection of 0.14 mg/hg RTF, acceptable recovery of 97.2-100.1%, and acceptable repeatability of 1.6-6.4% relative standard deviation. Additionally, the method was found to have no statistically significant bias compared with reference values for National Institute of Standards and Technology (NIST) 1849a certified reference material (CRM) (p-value = 0.95) and 1869 CRM (p-value = 0.31), and with results from AOAC 997.05 (p-value = 0.10).
    CONCLUSIONS: A recent review of the method and validation data by the Stakeholder Program on Infant Formula and Adult Nutritionals (SPIFAN) Expert Review Panel (ERP) found that this method met all the criteria for analysis of taurine specified in SMPR 2014.013 and voted to adopt this method as First Action AOAC Official Method 2022.03.
    HIGHLIGHTS: A method for the analysis of taurine in infant formulas and adult nutritionals by HILIC-MS/MS is described. A single laboratory validation study demonstrated the applicability of the method to meet requirements of SMPR 2014.013. In December 2022, the SPIFAN ERP voted to adopt this method as First Action AOAC Official Method 2022.03.
  17. Se Pu. 2023 Jul;41(7): 591-601
      Antibacterials represent a pharmaceutical class that is extensively used and consumed worldwide. The presence of a large number of antibacterial agents in water could result in antibiotic resistance. Thus, the development of a fast, accurate, and high-throughput method to analyze these emerging contaminants in water is necessary. Herein, a method was developed to achieve the simultaneous determination of 43 antibacterials from nine pharmaceutical categories (i.e., sulfonamides, quinolones, fluoroquinolones, tetracyclines, lincosamides, macrolides, nitroimidazoles, diterpenes, and dihydrofolate reductase inhibitors) in water using automatic sample loading-solid phase extraction (SPE)-ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Because the properties of these 43 antibacterials are quite different, the main objective of this work is to develop an extraction procedure that would enable the simultaneous analysis of a wide range of multiclass antibacterials. Given this context, the work presented in this paper optimized the SPE cartridge type, pH, and sample loading amount. Multiresidue extraction was performed as follows. The water samples were filtered through 0.45 μm filter membranes, added with Na2EDTA and NaH2PO4, and pH-adjusted to 2.34 using H3PO4. The solutions were then mixed with the internal standards. An automatic sample loading device fabricated by the authors was used for sample loading, and Oasis HLB cartridges were used for enrichment and purification. The optimized UPLC conditions were as follows: chromatographic column, Waters Acquity UPLC BEH C18 column (50 mm×2.1 mm, 1.7 μm); mobile phases, methanol-acetonitrile (2∶8, v/v) solution containing 0.1% formic acid and 0.1% formic acid aqueous solution; flow rate, 0.3 mL/min; injection volume, 10 μL. The compounds were step scanned using an electrospray ionization source in the positive and multiple-reaction monitoring (MRM) modes, and analyzed by internal and external standard methods. The results showed that the 43 compounds achieved high linearity in their respective linear ranges, with correlation coefficients (r2) greater than 0.996. The limits of detection (LODs) of the 43 antibacterial agents ranged from 0.004 ng/L to 1.000 ng/L, and their limits of quantification (LOQs) ranged from 0.012 ng/L to 3.000 ng/L. The average recoveries ranged from 53.7% to 130.4%, and the relative standard deviations (RSDs) were between 0.9% and 13.2%. The method was successfully applied to the determination of six tap water samples from different districts and six water samples obtained from the Jiangyin section of the Yangtze River and Xicheng Canal. No antibacterial compound was detected in any of the tap water samples, but a total of 20 antibacterial compounds were detected in the river and canal water samples. Among these compounds, sulfamethoxazole showed the highest mass concentrations, ranging from 8.92 to 11.03 ng/L. The types and contents of antibacterials detected in the Xicheng Canal were greater than those found in the Yangtze River, and two kinds of diterpenes, namely tiamulin and valnemulin, were found easily and commonly in water sample. The findings indicate that antibacterial agents are widespread in environmental waters. The developed method is accurate, sensitive, rapid, and suitable for the detection of the 43 antibacterial compounds in water samples.
    Keywords:  antibacterial residue; automatic sample loading; solid phase extraction (SPE); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); water body
  18. Se Pu. 2023 Jul;41(7): 582-590
      Bisphenols are endocrine disruptors that are characterized with bioaccumulation, persistence, and estrogenic activity. Even low contents of bisphenols can exert adverse effects on human health and the ecological environment. Herein, a method combining accelerated solvent extraction and solid-phase extraction purification with ultra performance liquid chromatography-tandem mass spectrometry was developed for the accurate detection of bisphenol A (BPA), bisphenol B (BPB), bisphenol F (BPF), bisphenol S (BPS), bisphenol Z (BPZ), bisphenol AF (BPAF), and bisphenol AP (BPAP) in sediments. The mass spectrometric parameters of the seven bisphenols were optimized, and the response values, separation effects, and chromatographic peak shapes of the target compounds were compared under three different mobile phase conditions. The sediment samples were pretreated by accelerated solvent extraction, and orthogonal tests were used to optimize the extraction solvent, extraction temperature, and cycle number. The results showed that the use of 0.05% (v/v) ammonia and acetonitrile as the mobile phase for gradient elution could rapidly separate the seven bisphenols on an Acquity UPLC BEH C18 column (100 mm×2.1 mm, 1.7 μm). The gradient program was as follows: 0-2 min, 60%A; 2-6 min, 60%A-40%A; 6-6.5 min, 40%A; 6.5-7 min, 40%A-60%A; 7-8 min, 60%A. Orthogonal experiments indicated that the optimal extraction conditions were as follows: extraction solvent of acetonitrile, extraction temperature of 100 ℃, and cycle number of three. The seven bisphenols showed good linearity in the range of 1.0-200 μg/L, with correlation coefficients (r2) greater than 0.999, and the limits of detection were 0.01-0.3 ng/g. The recoveries for the seven bisphenols ranged from 74.9% to 102.8% at three spiking levels (2.0, 10, 20 ng/g), with relative standard deviations ranging from 6.2% to 10.3%. The established method was applied to detect the seven bisphenols in sediment samples collected from Luoma Lake and its inflow rivers. BPA, BPB, BPF, BPS, and BPAF were detected in the sediments of the lake, and BPA, BPF, and BPS were detected in the sediments of its inflow rivers. The detection frequency of BPA and BPF was 100%, and the contents of these bisphenols in the sediment were 11.9-38.0 ng/g and 11.0-27.3 ng/g, respectively. The developed method is simple, rapid with high accuracy and precision, and is suitable for the determination of the seven bisphenols in sediment.
    Keywords:  accelerated solvent extraction (ASE); bisphenols; orthogonal test; sediment; solid-phase extraction (SPE); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  19. Molecules. 2023 Jun 08. pii: 4656. [Epub ahead of print]28(12):
      Cissus quadrangularis is a nutrient-rich plant with a history of use in traditional medicine. It boasts a diverse range of polyphenols, including quercetin, resveratrol, β-sitosterol, myricetin, and other compounds. We developed and validated a sensitive LC-MS/MS method to quantify quercetin and t-res biomarkers in rat serum and applied this method to pharmacokinetic and stability studies. The mass spectrometer was set to negative ionization mode for the quantification of quercetin and t-res. Phenomenex Luna (C18(2), 100 A, 75 × 4.6 mm, 3 µ) column was utilized to separate the analytes using an isocratic mobile phase consisting of methanol and 0.1% formic acid in water (82:18). Validation of the method was performed using various parameters, including linearity, specificity, accuracy, stability, intra-day, inter-day precision, and the matrix effect. There was no observed significant endogenous interference from the blank serum. The analysis was completed within 5.0 min for each run, and the lower limit of quantification was 5 ng/mL. The calibration curves showed a linear range with a high correlation coefficient (r2 > 0.99). The precision for intra- and inter-day assays showed relative standard deviations from 3.32% to 8.86% and 4.35% to 9.61%, respectively. The analytes in rat serum were stable during bench-top, freeze-thaw, and autosampler (-4 °C) stability studies. After oral administration, the analytes showed rapid absorption but underwent metabolism in rat liver microsomes despite being stable in simulated gastric and intestinal fluids. Intragastric administration resulted in higher absorption of quercetin and t-res, with greater Cmax, shorter half-life, and improved elimination. No prior research has been conducted on the oral pharmacokinetics and stability of anti-diabetic compounds in the Ethanolic extract of Cissus quadrangularis EECQ, making this the first report. Our findings can provide the knowledge of EECQ's bioanalysis and pharmacokinetic properties which is useful for future clinical trials.
    Keywords:  Cissus quadrangularis; LC-MS/MS; pharmacokinetics; quercetin; trans-resveratrol; validation
  20. Adv Lab Med. 2022 Oct;3(3): 263-281
      Objectives: Administration of busulfan is extending rapidly as a part of a conditioning regimen in patients undergoing hematopoietic stem cell transplantation (HSCT). Monitoring blood plasma levels of busulfan is recommended for identifying the optimal dose in patients and for minimizing toxicity. The aim of this research was to validate a simple, rapid, and cost-effective analytical tool for measuring busulfan in human plasma that would be suitable for routine clinical use. This novel tool was based on liquid chromatography coupled to mass spectrometry.Methods: Human plasma samples were prepared using a one-step protein precipitation protocol. These samples were then resolved by isocratic elution in a C18 column. The mobile phase consisted 2 mM ammonium acetate and 0.1% formic acid dissolved in a 30:70 ratio of methanol/water. Busulfan-d8 was used as the internal standard.
    Results: The run time was optimized at 1.6 min. Standard curves were linear from 0.03 to 5 mg/L. The coefficient of variation (%CV) was less than 8%. The accuracy of this method had an acceptable bias that fell within 85-115% range. No interference between busulfan and the interfering compound hemoglobin, lipemia, or bilirubin not even at the highest concentrations of compound was tested. Neither carryover nor matrix effects were observed using this method. The area under the plasma drug concentration-time curves obtained for 15 pediatric patients who received busulfan therapy prior to HSCT were analyzed and correlated properly with the administered doses.
    Conclusions: This method was successfully validated and was found to be robust enough for therapeutic drug monitoring in a clinical setting.
    Keywords:  hematopoietic stem cell transplantation; mass spectrometry platform; method validation; therapeutic drug monitoring
  21. Metabolomics. 2023 06 25. 19(7): 63
      INTRODUCTION: Helminths are parasitic worms that infect millions of people worldwide and secrete a variety of excretory-secretory products (ESPs), including proteins, peptides, and small molecules. Despite this, there is currently no comprehensive review article on cataloging small molecules from helminths, particularly focusing on the different classes of metabolites (polar and lipid molecules) identified from the ESP and somatic tissue extracts of helminths that were studied in isolation from their hosts.OBJECTIVE: This review aims to provide a comprehensive assessment of the metabolomics and lipidomics studies of parasitic helminths using all available analytical platforms.
    METHOD: To achieve this objective, we conducted a meta-analysis of the identification and characterization tools, metabolomics approaches, metabolomics standard initiative (MSI) levels, software, and databases commonly applied in helminth metabolomics studies published until November 2021.
    RESULT: This review analyzed 29 studies reporting the metabolomic assessment of ESPs and somatic tissue extracts of 17 helminth species grown under ex vivo/in vitro culture conditions. Of these 29 studies, 19 achieved the highest level of metabolite identification (MSI level-1), while the remaining studies reported MSI level-2 identification. Only 155 small molecule metabolites, including polar and lipids, were identified using MSI level-1 characterization protocols from various helminth species. Despite the significant advances made possible by the 'omics' technology, standardized software and helminth-specific metabolomics databases remain significant challenges in this field. Overall, this review highlights the potential for future studies to better understand the diverse range of small molecules that helminths produce and leverage their unique metabolomic features to develop novel treatment options.
    Keywords:  Helminths; Lipidomics; Metabolomics; Parasites
  22. Biochem J. 2023 Jun 28. 480(12): 891-908
      Metabolomics is a powerful research discovery tool with the potential to measure hundreds to low thousands of metabolites. In this review, we discuss the application of GC-MS and LC-MS in discovery-based metabolomics research, we define metabolomics workflows and we highlight considerations that need to be addressed in order to generate robust and reproducible data. We stress that metabolomics is now routinely applied across the biological sciences to study microbiomes from relatively simple microbial systems to their complex interactions within consortia in the host and the environment and highlight this in a range of biological species and mammalian systems including humans. However, challenges do still exist that need to be overcome to maximise the potential for metabolomics to help us understanding biological systems. To demonstrate the potential of the approach we discuss the application of metabolomics in two broad research areas: (1) synthetic biology to increase the production of high-value fine chemicals and reduction in secondary by-products and (2) gut microbial interaction with the human host. While burgeoning in importance, the latter is still in its infancy and will benefit from the development of tools to detangle host-gut-microbial interactions and their impact on human health and diseases.
    Keywords:  metabolites; metabolomics; microbiome; multi-omics; synthetic biology
  23. ACS Meas Sci Au. 2023 Jun 21. 3(3): 200-207
      Anthocyanins are a subclass of plant-derived flavonoids that demonstrate immense structural heterogeneity which is challenging to capture in complex extracts by traditional liquid chromatography-mass spectrometry (MS)-based approaches. Here, we investigate direct injection ion mobility-MS as a rapid analytical tool to characterize anthocyanin structural features in red cabbage (Brassica oleracea) extracts. Within a 1.5 min sample run time, we observe localization of structurally similar anthocyanins and their isobars into discrete drift time regions based upon their degree of chemical modifications. Furthermore, drift time-aligned fragmentation enables simultaneous collection of MS, MS/MS, and collisional cross-section data for individual anthocyanin species down to a low picomole scale to generate structural identifiers for rapid identity confirmation. We finally identify anthocyanins in three other Brassica oleracea extracts based on red cabbage anthocyanin identifiers to demonstrate our high-throughput approach. Direct injection ion mobility-MS therefore provides wholistic structural information on structurally similar, and even isobaric, anthocyanins in complex plant extracts, which can inform the nutritional value of a plant and bolster drug discovery pipelines.
  24. Molecules. 2023 Jun 17. pii: 4829. [Epub ahead of print]28(12):
      The large quantity of olive roots resulting from a large number of old and unfruitful trees encouraged us to look for ways of adding value to these roots. For this reason, the current research work is devoted to the valorization of olive roots by identifying active phytochemicals and assessing their biological activities, including the cytotoxicity and antiviral potential of different extracts from the Olea europaea Chemlali cultivar. The extract, obtained by ultrasonic extraction, was analyzed using the liquid chromatography-mass spectrometry technique (LC-MS). The cytotoxicity was evaluated through the use of the microculture tetrazolium assay (MTT) against VERO cells. Subsequently, the antiviral activity was determined for HHV-1 (Human Herpesvirus type 1) and CVB3 (Coxsackievirus B3) replication in the infected VERO cells. LC-MS analysis allowed the identification of 40 compounds, classified as secoiridoids (53%), organic acids (13%), iridoids (10%), lignans (8%), caffeoylphenylethanoid (5%), phenylethanoids (5%),sugars and derivatives (2%), phenolic acids (2%), and flavonoids (2%). It was found that extracts were not toxic to the VERO cells. Moreover, the extracts did not influence the appearance of HHV-1 or CVB3 cytopathic effects in the infected VERO cells and failed to decrease the viral infectious titer.
    Keywords:  LC-MS; biological activities; olive roots; phenolic compounds; ultrasonic extraction
  25. Bioanalysis. 2023 Jun 24.
      Background: Workplace drug testing primarily relies on urine analysis, targeting multiple compounds with varying physicochemical characteristics. Biocompatible solid-phase microextraction (BioSPME) is a miniaturized solid-phase extraction technique that enables the simultaneous extraction and preconcentration of analytes directly from the biological matrix. Methods: The BioSPME procedure consisted of the sequential extraction of 50-μl urine samples using LC Tips C18 in basic and acidic pH, followed by desorption with methanol and n-hexane, respectively. The extracts were analyzed by ultra-performance LC-MS/MS. Results: Intra-day precision was 1.2-8.6% and inter-day precision was 1.8-14.2%. Accuracy was 96.8-107.4%. The extraction yields were 62.8-109.4%. The matrix effects were -3.98% to 1%. Conclusion: BioSPME shows promise as an alternative method for preparing urine samples prior to drug measurement by ultra-performance LC-MS/MS.
    Keywords:  BioSPME; UPLC–MS/MS; drugs of abuse; urine; workplace drug testing
  26. Pharmaceuticals (Basel). 2023 Jun 19. pii: 903. [Epub ahead of print]16(6):
      BACKGROUND: Opioids are considered the cornerstone of pain management: they show good efficacy as a first-line therapy for moderate to severe cancer pain. Since pharmacokinetic/pharmacodynamic information about the tissue-specific effect and toxicity of opioids is still scarce, their quantification in post-mortem autoptic specimens could give interesting insights.METHODS: We describe an ultra-high-performance liquid chromatography coupled with tandem mass spectrometry method for the simultaneous quantification of methadone, morphine, oxycodone, hydrocodone, oxymorphone, hydromorphone and fentanyl in several tissues: liver, brain, kidney, abdominal adipose tissue, lung and blood plasma. The presented method has been applied on 28 autoptic samples from different organs obtained from four deceased PLWH who used opioids for palliative care during terminal disease.
    RESULTS: Sample preparation was based on tissue weighing, disruption, sonication with drug extraction medium and a protein precipitation protocol. The extracts were then dried, reconstituted and injected onto the LX50 QSight 220 (Perkin Elmer, Milan, Italy) system. Separation was obtained by a 7 min gradient run at 40 °C with a Kinetex Biphenyl 2.6 µm, 2.1 × 100 mm. Concerning the analyzed samples, higher opioids concentrations were observed in tissues than in plasma. Particularly, O-MOR and O-COD showed higher concentrations in kidney and liver than other tissues (>15-20 times greater) and blood plasma (>100 times greater).
    CONCLUSIONS: Results in terms of linearity, accuracy, precision, recovery and matrix effect fitted the recommendations of FDA and EMA guidelines, and the sensitivity was high enough to allow successful application on human autoptic specimens from an ethically approved clinical study, confirming its eligibility for post-mortem pharmacological/toxicological studies.
    Keywords:  LC-MS; fentanyl; morphine; opioids; tissue