bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒04‒30
25 papers selected by
Sofia Costa

  1. Metabolites. 2023 Mar 23. pii: 463. [Epub ahead of print]13(4):
      Untargeted metabolomics is a powerful tool for measuring and understanding complex biological chemistries. However, employment, bioinformatics and downstream analysis of mass spectrometry (MS) data can be daunting for inexperienced users. Numerous open-source and free-to-use data processing and analysis tools exist for various untargeted MS approaches, including liquid chromatography (LC), but choosing the 'correct' pipeline isn't straight-forward. This tutorial, in conjunction with a user-friendly online guide presents a workflow for connecting these tools to process, analyse and annotate various untargeted MS datasets. The workflow is intended to guide exploratory analysis in order to inform decision-making regarding costly and time-consuming downstream targeted MS approaches. We provide practical advice concerning experimental design, organisation of data and downstream analysis, and offer details on sharing and storing valuable MS data for posterity. The workflow is editable and modular, allowing flexibility for updated/changing methodologies and increased clarity and detail as user participation becomes more common. Hence, the authors welcome contributions and improvements to the workflow via the online repository. We believe that this workflow will streamline and condense complex mass-spectrometry approaches into easier, more manageable, analyses thereby generating opportunities for researchers previously discouraged by inaccessible and overly complicated software.
    Keywords:  bioinformatics; mass-spectrometry; metabolomics; open-source; untargeted
  2. Molecules. 2023 Apr 14. pii: 3483. [Epub ahead of print]28(8):
      The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.
    Keywords:  ion mobility spectrometry; lipid identification; lipidomics; mass spectrometry; software
  3. Se Pu. 2023 May 08. 41(5): 397-408
      An analytical method combining high-throughput automatic solid-phase extraction with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed to determine 16 antibiotics (macrolides, tetracyclines, quinolones, and sulfonamides) and 4 β-agonists (terbutaline, salbutamol, ractopamine, and clenbuterol) in human urine samples. After thawing at room temperature, 1 mL of urine was sampled and the internal standard was added, followed by the addition of 200 μL ammonium acetate buffer and 20 μL β-glucuronidase, and the mixture was incubated at 37 ℃ overnight. Automatic solid-phase extraction was used to extract the target compounds from the urine samples, and the recoveries were compared using different solid-phase extraction 96-well plates (PRiME MCX, Sep-Pak C18, PRiME HLB), types and volumes of rinse solutions and eluents. Satisfactory recoveries of the 20 target compounds were obtained using the Oasis PRiME HLB 96-well plate, with 1.5 mL 10% (v/v) methanol aqueous solution and 2.0 mL methanol as the rinse solution and eluent, respectively. The eluent was concentrated under nitrogen gas at 45 ℃, and the recoveries of the target compounds were compared under different conditions (completely or almost dry, drying to 1 mL, and adding water as a protective agent), and the recovery rate was optimal when water was added as a protective agent. In this study, two types of analytical columns (ACQUITY BEH C18 and ACQUITY HSS T3) and different gradient elution procedures and mobile phases were compared. The optimal chromatographic effect was realized using an HSS T3 column (100 mm×3.0 mm, 1.8 μm) and 0.1% (v/v) formic acid aqueous solution-0.1% (v/v) formic acid in acetonitrile as the mobile phase in gradient elution at a flow rate of 0.3 mL/min. Comparing the peaks observed using different proportions of methanol aqueous solution and the initial mobile phase as the injection solvent revealed that 30% (v/v) methanol aqueous solution was the optimal solution in terms of peak shape and signal-to-noise ratio. MS was conducted using positive electrospray ionization (ESI+) in multiple reaction monitoring (MRM) mode, and the MS parameters were optimized, including the curtain (CUR) and collision gases (CAD). The standard curve obtained using this method exhibited a good linearity (correlation coefficient>0.997), and the respective limits of detection and quantification were 0.02-0.12 ng/mL and 0.06-0.41 ng/mL. At spiked levels of 0.25, 2.5, and 12.5 ng/mL, the recoveries were in the range of 81.7%-120.0% (except that of tetracycline), the intra- and inter-day RSDs (n=6) were 1.1%-11.0% and 1.2%-13.0%, respectively. Azithromycin, trimethoprim, terbutaline, salbutamol, ractopamine, and clenbuterol displayed moderate matrix effects, but all targets exhibited weak matrix effects after correction using the isotope internal standard. To evaluate the accuracy of this method, BCR-503 (containing salbutamol and clenbuterol) and internal quality control samples were used and the concentrations of salbutamol and clenbuterol were within the reference ranges. Additionally, the mean concentrations of the 20 target compounds of two different internal quality control samples after 7 measurements were in the ranges of 0.44-0.59 ng/mL (0.5 ng/mL) and 1.72-2.16 ng/mL (2.0 ng/mL), respectively, which were satisfactory. In this study, the analytical method employed automatic sample pretreatment with a 96-well solid-phase extraction plate, and the detection efficiency was considerably improved. This method displays the advantages of simple operation, ideal recovery, a high sensitivity and weak matrix effect, which satisfies the requirements for the simultaneous determination of 16 antibiotics and 4 β-agonists in human urine samples. This study provides a crucial method for use in monitoring antibiotics and β-agonists in human urine and studying their exposure characteristics and health risks.
    Keywords:  antibiotics; solid-phase extraction (SPE); ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); urine; β-agonists
  4. J Am Soc Mass Spectrom. 2023 Apr 25.
      The collection of profile data is standard practice within the field of mass spectrometry (MS). However, profile data collection often results in large data files that require extensive processing times, especially in mass spectrometry imaging (MSI) studies where thousands of high-resolution scans are recorded. Natively collecting centroid MS data is an alternative that effectively reduces both the resulting file size and the data processing time. Herein, high-resolution accurate mass (HRAM) Orbitrap MSI data on mouse liver tissue sections without automatic gain control (AGC) were natively collected in both profile and centroid modes and compared based on the file size and processing time. Additionally, centroid data were evaluated against the profile data with regard to the spectra integrity, mass measurement accuracy (MMA), and the number of lipid annotations to ensure that centroid data did not compromise the data quality. For both native and postacquisition centroided data, the variation in mass measurement accuracy decreased relative to the profile data collection. Furthermore, centroid data collection increased the number of METASPACE database annotations indicating higher sensitivity and greater accuracy for lipid annotation compared to native profile data collection. Profile MSI data was shown to have a higher likelihood of false positive identifications due to an increased number of data points on either side of the peaks, whereas the same trend was not observed in data collected in native centroid data collection. This publication explores and explains the importance in properly centroiding MSI data, either natively or by adequate centroiding methods, to obtain the most accurate information and come to the best conclusions. These data support that natively collecting centroid data significantly improves MMA to sub-ppm levels without AGC and reduces false positive annotations.
    Keywords:  IR-MALDESI; Orbitrap; automatic gain control; centroid; mass measurement accuracy; mass spectrometry imaging
  5. Int J Mol Sci. 2023 Apr 15. pii: 7332. [Epub ahead of print]24(8):
      Amino acid (AA) analysis is important in biochemistry, food science, and clinical medicine. However, due to intrinsic limitations, AAs usually require derivatization to improve their separation and determination. Here, we present a liquid chromatography-mass spectrometry (LC-MS) method for the derivatization of AAs using the simple agent urea. The reactions proceed quantitatively under a wide range of conditions without any pretreatment steps. Urea-derivatized products (carbamoyl amino acids) of 20 AAs exhibit better separation on reversed-phase columns and increased response in a UV detector compared to underivatized ones. We applied this approach to AA analysis in complex samples using a cell culture media as a model, and it showed potential for the determination of oligopeptides. This fast, simple, and inexpensive method should be useful for AA analysis in complex samples.
    Keywords:  LC-MS; amino acids; derivatization; quantitative analysis; urea
  6. Anal Chem. 2023 Apr 28.
      For a large-scale metabolomics study, sample collection, preparation, and analysis may last several days, months, or even (intermittently) over years. This may lead to apparent batch effects in the acquired metabolomics data due to variability in instrument status, environmental conditions, or experimental operators. Batch effects may confound the true biological relationships among metabolites and thus obscure real metabolic changes. At present, most of the commonly used batch effect correction (BEC) methods are based on quality control (QC) samples, which require sufficient and stable QC samples. However, the quality of the QC samples may deteriorate if the experiment lasts for a long time. Alternatively, isotope-labeled internal standards have been used, but they generally do not provide good coverage of the metabolome. On the other hand, BEC can also be conducted through a data-driven method, in which no QC sample is needed. Here, we propose a novel data-driven BEC method, namely, CordBat, to achieve concordance between each batch of samples. In the proposed CordBat method, a reference batch is first selected from all batches of data, and the remaining batches are referred to as "other batches." The reference batch serves as the baseline for the batch adjustment by providing a coordinate of correlation between metabolites. Next, a Gaussian graphical model is built on the combined dataset of reference and other batches, and finally, BEC is achieved by optimizing the correction coefficients in the other batches so that the correlation between metabolites of each batch and their combinations are in concordance with that of the reference batch. Three real-world metabolomics datasets are used to evaluate the performance of CordBat by comparing it with five commonly used BEC methods. The present experimental results showed the effectiveness of CordBat in batch effect removal and the concordance of correlation between metabolites after BEC. CordBat was found to be comparable to the QC-based methods and achieved better performance in the preservation of biological effects. The proposed CordBat method may serve as an alternative BEC method for large-scale metabolomics that lack proper QC samples.
  7. Se Pu. 2023 May 08. 41(5): 426-433
      A novel method was developed for the simultaneous determination of eight cannabinoids in six types of food matrices, including chocolate, fondant, biscuit, beverage, cookie and baijiu, using ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The sample extraction and cleanup steps were optimized, and various purification methods were investigated to remove the oil matrix and glue in chocolate and fudge, respectively. Enhanced matrix removal-lipid adsorbent (EMR-Lipid) provided efficient, selective cleanup of the evaluated matrices. The sample was extracted using acetonitrile, followed by EMR-Lipid cleanup, and then dried using anhydrous sodium sulfate. The acetonitrile layer was concentrated by nitrogen to near-dry after 100 μL 10% glycerol in methanol was added to improve the recovery by reducing loss during concentration under the stream of nitrogen gas. Eight cannabinoids were separated using a Waters ACQUITY UPLC BEH Shield RP18 column (100 mm×3.0 mm, 1.7 μm). The responses of the cannabinoids in the positive and negative ionization modes were investigated and optimized, and the responses were superior in the negative ion mode compared to those in the positive ion mode. MS detection was performed in the multi-reaction monitoring (MRM) mode using an electrospray source in the negative ion mode. The cannabinoids were quantified using an external standard with matrix calibration curves to reduce the influences of the matrix effects on the quantitative results. The developed method was verified, and the conditions of sample pretreatment were also optimized. The calibration curves of tetrahydrocannabinol, cannabidivarin, tetrahydrocannabivarin, and cannabigerol and those of cannabidiol, cannabinol, cannabidiolic acid, and tetrahydrocannabinolic acid exhibited good linearities, with r>0.995, in the ranges of 2-200 and 0.4-40 ng/mL, respectively. The respective limits of detection (LODs, S/N=3) and quantification (LOQs, S/N=10) of tetrahydrocannabinol, cannabidivarin, tetrahydrocannabivarin, and cannabigerol were 4 and 10 μg/kg, and those of cannabidiol, cannabinol, cannabidiolic acid, and tetrahydrocannabinolic acid were 0.8 and 2 μg/kg. The average recoveries of the cannabinoids were 82.0%-114.9% under three spiked levels with corresponding relative standard deviations (RSDs) of <15% (n=6). EMR-Lipid provided efficient, selective cleanups of food matrices with good accuracy. The method is sensitive, rapid, accurate, simple to execute, and it is suitable for the determination of cannabinol compounds in typical food matrices.
    Keywords:  cannabinoids; enhanced matrix removal-lipid cleaning adsorbent (EMR-Lipid); foods; ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  8. Se Pu. 2023 May 08. 41(5): 443-449
      Fatty acids not only form phospholipids that contribute to the formation of cell membranes but also participate in many metabolic activities, such as energy storage and cell signal transduction. The liver plays a key role in the synthesis and metabolism of fatty acids. The composition and contents of fatty acids in the liver are closely related to body health. Most fatty acid-detection methods require a large sample size and can detect only a small number of fatty acids. Therefore, a sensitive and efficient method to determine fatty acids in the liver is urgently required. Herein, a method based on gas chromatography-mass spectrometry (GC-MS) was established for the simultaneous determination of 39 fatty acids in 1.1 mg of liver tissue. Different extraction methods and derivatization conditions were compared to develop an optimal sample-treatment method. The performance of two different columns in separating the target fatty acids were also compared. A total of 10 mg of liver was added to 450 μL of normal saline and ground at -35 ℃ to obtain a homogenate. Next, 50 μL of the homogenate (equivalent to 1.1 mg of liver) was added with 750 μL of chloroform-methanol (1∶2, v/v) to extract total fatty acids. The fatty acid extracts were dried under nitrogen, and then derivatized at 100 ℃ for 90 min after being added with methanol containing 5% sulfuric acid. The fatty acid methyl esters were extracted with hexane and then separated on an SP-2560 capillary column (100 m×0.25 mm×0.2 μm; Supelco, USA) via GC-MS. The results revealed that all 39 fatty acid methyl esters detected had good linearities in the certain mass concentration ranges with correlation coefficients (R2) greater than 0.9940. The limits of detection (LOD) and quantification (LOQ) of these methyl esters in the liver were 2-272 ng/mg and 7-906 ng/mg, respectively. The accuracy and precision of the method were evaluated by spiking the liver homogenate with tridecylic acid and eicosanoic acid at low (0.09 μg/mg), moderate (0.90 μg/mg), and high (5.40 μg/mg) concentration levels. The recoveries ranged from 82.4% to 101.0% with an intraday relative standard deviations (RSDs) (n=5) of 3.2%-12.0% and interday RSDs (n=3) of 5.4%-13.4%. The method was successfully applied to detect fatty acids in the livers of four healthy male Sprague-Dawley (SD) rats and four male SD rats with abnormal liver function induced by perfluorooctane sulfonate (PFOS). PFOS is a persistent organic pollutant. Twenty-six fatty acids were detected in the livers of both groups. Among the fatty acids investigated, pentadecanoic acid (C15∶0), γ-linolenic acid (C18∶3n6), and elaidic acid (C18∶1n9t) cannot be detected by the methods reported in the literature. By contrast, the method developed in this study could separate the isomers of oleic acid (elaidic acid, C18∶1n9t; oleic acid, C18∶1n9c) and linolenic acid (linolelaidic acid, C18∶2n6t; linoleic acid, C18∶2n6c). In conclusion, the developed method is simple and can detect a large number of fatty acids using small sample amounts and few reagents. More importantly, it could successfully separate fatty acid isomers. These findings indicate that the developed method is suitable for the detection of fatty acid composition and contents in the liver in clinical and experimental research.
    Keywords:  fatty acids; gas chromatography-mass spectrometry (GC-MS); liver
  9. Antibiotics (Basel). 2023 Apr 06. pii: 719. [Epub ahead of print]12(4):
      Meropenem (MRP)-Vaborbactam (VBR) is a novel beta-lactam/beta-lactamase inhibitor used for the management of difficult-to-treat Gram-negative infections. Among critically ill patients, MRP-VBR shows remarkable inter-individual variability in pharmacokinetic behavior, thus justifying the implementation of therapeutic drug monitoring (TDM) for improving real-time management in different challenging scenarios. In this study, we developed and validated a fast and sensitive Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) method for the simultaneous quantification of MRP and VBR in human plasma microsamples of 3 microliters. The analysis required only a single-step sample preparation and was performed by means of a fast chromatographic run of 4 min, followed by positive electrospray ionization and detection on a high-sensitivity triple quadrupole tandem mass spectrometer operated in multiple reaction monitoring modes. The straightforward analytical procedure was successfully validated, based on the EMA guidelines, in terms of specificity, sensitivity, linearity, precision, accuracy, matrix effect, extraction recovery, the limit of quantification, and stability. The novel method was successfully applied for simultaneously measuring MRP and VBR concentrations in more than 42 plasma samples collected from critically ill patients affected by carbapenem-resistant Gram-negative bacteria infections.
    Keywords:  liquid chromatography–tandem mass spectrometry; meropenem; plasma micro samples; therapeutic drug monitoring; vaborbactam
  10. Se Pu. 2023 May 08. 41(5): 434-442
      Because of the widespread application of anesthetic drugs in the fields of animal breeding and transportation, demand for the rapid, sensitive detection of anesthetic drugs in animal meat is increasing. The complex animal meat matrix contains various interfering substances, such as proteins, fats, and phospholipids, along with anesthetic drug residues at very low concentrations. Therefore, adopting appropriate pretreatment methods is necessary to improve the sensitivity of detection. In this study, a rapid, accurate analytical method based on ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and solid phase extraction (SPE) was established to determine the contents of 18 caines in animal meat. The MS parameters, such as the collision energies of 18 caines, were optimized. Furthermore, the chromatographic separation conditions and response intensities of the caine in different mobile phases were compared. The effects of different pretreatment conditions on the extraction efficiencies of the 18 caines in meat samples and those of different purification conditions, such as extraction solvent, SPE column, and dimethylsulfoxide (DMSO) dosage, on their recoveries were investigated. Combined with the external standard method, the 18 caines in meat were successfully quantified. Sample pretreatment is a three-step process. First, in ultrasound-assisted extraction, 2.0 g samples were added to 2.0 mL water and extracted using 10 mL 0.1% (v/v) formic acid in acetonitrile under ultrasound conditions for 10 min. SPE was then performed using an Oasis PRIME HLB column. Finally, DMSO-assisted concentration was employed: the organic layer was collected and dried at 40 ℃ under a stream of N2 gas with the addition of 100 μL DMSO. Acetonitrile-water (1∶9, v/v) was added to the residue to yield a final volume of 1.0 mL for use in UPLC-MS/MS. The 18 caines were separated using an HSS T3 (100 mm×2.1 mm, 1.8 μm) column with 0.1% (v/v) formic acid in water (containing 0.02 mmol/L ammonium acetate) and methanol as mobile phases. Samples were detected using an electrospray ion source (ESI) in the positive ion and multiple reaction monitoring (MRM) modes during UPLC-MS/MS. Under the optimized conditions, the 18 target caine anesthetics displayed good linearities in the range of 1.00-50.0 μg/L, and the correlation coefficients (R2) were >0.999. The respective limits of detection (LODs) and quantification (LOQs) were 0.2-0.5 μg/kg, and 0.6-1.5 μg/kg. In pork, beef, and mutton samples, the recoveries obtained at three spiked levels were 83.4%-100.4% with relative standard deviations (RSDs) of 3.1%-8.5%. This simple, rapid, sensitive method may be applied in the detection of 18 caine anesthetics in animal meat and may provide technical support to the food safety department in China in monitoring the residues of caine anesthetics in animal meat.
    Keywords:  animal meat; caine anesthetics; solid phase extraction (SPE); ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  11. Methods Enzymol. 2023 ;pii: S0076-6879(22)00392-5. [Epub ahead of print]683 191-224
      Diacylglycerols (DAGs) are anabolic precursors to membrane lipid and storage triacylglycerol biosynthesis, metabolic intermediates of lipid catabolism, and potent cellular signaling molecules. The different DAG molecular species that accumulate over development or in different tissues reflect the changing aspects of cellular lipid metabolism. Consequently, an accurate determination of DAG molecular species in biological samples is essential to understand various metabolic processes and their diagnostic relevance. However, quantification of DAG molecular species in various biological samples represents a challenging task because of their low abundance, hydrophobicity, and instability. This chapter describes the most common chromatographic (TLC and HPLC) and mass spectrometry (MS) methods used to analyze DAG molecular species. In addition, we directly compared the three methods using DAG obtained by phospholipase C hydrolysis of phosphatidylcholine purified from a Nicotiana benthamiana leaf extract. We conclude that each method identified similar major molecular species, however, the exact levels of those varied mainly due to sensitivity of the technique, differences in sample preparation, and processing. This chapter provides three different methods to analyze DAG molecular species, and the discussion of the benefits and challenges of each technique will aid in choosing the right method for your analysis.
    Keywords:  Argentation chromatography; Diacylglycerol; Electrospray ionization mass spectrometry (ESI-MS); Evaporative light scatter detector (ELSD); Flow liquid scintillation counting (LSC); High performance liquid chromatography (HPLC); Lipid; Molecular species; Radioisotope; Thin-layer chromatography (TLC)
  12. J Chromatogr A. 2023 Apr 14. pii: S0021-9673(23)00220-0. [Epub ahead of print]1697 463994
      Monitoring the central carbon metabolism (CCM) network using liquid chromatography/mass spectrometry (LC-MS) analysis is hampered by the diverse chemical nature of its analytes, which are extremely difficult to analyze using single chromatographic conditions. Furthermore, CCM-related compounds present non-specific adsorption on metal surfaces, causing detrimental chromatographic effects and sensitivity loss. In this study, polar reversed-phase, mixed-mode (MMC), and zwitterionic hydrophilic interaction chromatography (HILIC) featuring low-adsorption hardware were investigated towards untargeted analysis of biological samples with a focus on energy metabolism-related analytes. Best results were achieved with sulfoalkylbetaine HILIC with different supports, where polymeric option featured the highest coverage and inert hybrid silica facilitated best throughput and kinetic performance at a cost of less selectivity for small carboxylic acids. MMC demonstrated excellent performance for strongly anionic analytes such as multiresidue phosphates. The obtained experimental data also suggested that an additional hydrophilic modulation might be necessary to facilitate better resolution of carboxylic acids in zHILIC mode, as found during the application of the developed method to study the effect of two different mutations on the energy metabolism of S. aureus.
    Keywords:  Central carbon metabolism; Low adsorption column hardware; Mixed-mode chromatography; Untargeted metabolomics; Zwitterionic HILIC
  13. J Chromatogr A. 2023 Apr 17. pii: S0021-9673(23)00227-3. [Epub ahead of print]1698 464001
      Reliable analysis of ultratrace antibiotics in bacterial cells may become a new means to elucidate the antibacterial mechanism, drug resistance and environmental fate. In this work, an ultrahigh-sensitive, accurate and enhanced liquid chromatography-tandem mass spectrometric method was first developed for chiral separation and detection of racemic closantel, as an antibacterial adjuvant. Optimizing acetonitrile-water-formic acid system that is compatible with mass spectrometry as a mobile phase, the baseline separation of two enantiomers was achieved by using EnantioPak® Y1-R chiral column, and the resolution of the two analytes was more than 1.95. Further adopt the strategy of postcolumn infusion of ammonia, the mobile phase pH was reversed from acidic condition suitable for the optimal chromatographic separation of R- and S-closantel to alkaline, so that closantel could realize efficient electrospray ionization under the preferred negative ion mode. The bacterial cells were subjected to be frozen-cracked, and the analytes were extracted with acetonitrile after clipping the pointed bottom of the Eppendorf tube into a new tube. The method was linear over concentration ranges of 0.5-50 pg/mL (r2≥0.99) for R- and S-closantel. The detection limits of target analytes were all 0.15 pg/mL in bacterial cells. The average recoveries of two enantiomers ranged from 81.2% to 107.8% with relative standard deviations below 15%. The method proposed might be important support for the deep research of the stereoselectivity of biological activity, toxicity and metabolism of closantel enantiomers.
    Keywords:  Bacteria; Closantel; Enantioseparation; Liquid chromatography-tandem mass spectrometry combined with postcolumn infusion; Ultratrace analysis
  14. Chem Commun (Camb). 2023 Apr 26.
      The microbiome has been identified to have a key role for the physiology of their human host. One of the major impacts is the clearance of bacterial pathogens. We have now developed a chemoselective probe methodology for the absolute quantification of short-chain fatty acids at low nM concentrations, with high reproducibility and spiked isotope labelled internal standards. Immobilization to magnetic beads allows for separation from the matrix and the tagged metabolites upon bioorthogonal cleavage can be analyzed via UHPLC-MS. The major advantage of our sensitive method is the simple combination with global metabolomics analysis as only a small sample volume is required. We have applied this chemical metabolomics strategy for targeted SCFA analysis combined with global metabolomics on gut microbiome co-cultures with Salmonella and investigated the effect of antibiotic treatment.
  15. Drug Test Anal. 2023 Apr 28.
      Separation and quantification of amphetamine enantiomers is commonly used to distinguish between consumption of prescription amphetamine (mostly S-amphetamine) and illicit forms of the drug (racemate). In this study, electromembrane extraction with prototype conductive vials was combined with ultra-high performance supercritical fluid chromatography (UHPSFC-MS/MS) to quantify R- and S-amphetamine in urine. Amphetamine was extracted from 100 μL urine, diluted with 25 μL internal standard solution and 175 μL 130 mM formic acid, across a supported liquid membrane (SLM) consisting of 9 μL of a 1:1(v/v) mixture of 2-nitrophenyloctyl ether (NPOE) and bis(2-ethylhexyl)phosphite (DEHPi) into an acceptor phase containing 300 μL 130 mM formic acid. The extraction was facilitated by the application of 30 V for 15 min. Enantiomeric separation was achieved using UHPSFC-MS/MS with a chiral stationary phase. The calibration range was 50-10 000 ng/mL for each enantiomer. The between-assay CV was ≤5%, within-assay CV ≤1.5% and bias within ±2%. Recoveries were 83-90% (CV ≤6%), and internal standard corrected matrix effects were 99-105 (CV≤2%). The matrix effects ranged from 96 to 98% (CV≤8%) when not corrected by the internal standard. The EME method was compared to a chiral routine method that employed liquid-liquid extraction (LLE) for sample preparation. Assay results were in agreement with the routine method, and the mean deviation between methods was 3%, ranging from -21% to 31%. Finally, sample preparation greenness was assessed using the AGREEprep tool, which resulted in a greenness score of 0.54 for conductive vial EME, opposed to 0.47 for semi-automated 96-well LLE.
  16. Nat Commun. 2023 Apr 28. 14(1): 2461
      Multidimensional measurements using state-of-the-art separations and mass spectrometry provide advantages in untargeted metabolomics analyses for studying biological and environmental bio-chemical processes. However, the lack of rapid analytical methods and robust algorithms for these heterogeneous data has limited its application. Here, we develop and evaluate a sensitive and high-throughput analytical and computational workflow to enable accurate metabolite profiling. Our workflow combines liquid chromatography, ion mobility spectrometry and data-independent acquisition mass spectrometry with PeakDecoder, a machine learning-based algorithm that learns to distinguish true co-elution and co-mobility from raw data and calculates metabolite identification error rates. We apply PeakDecoder for metabolite profiling of various engineered strains of Aspergillus pseudoterreus, Aspergillus niger, Pseudomonas putida and Rhodosporidium toruloides. Results, validated manually and against selected reaction monitoring and gas-chromatography platforms, show that 2683 features could be confidently annotated and quantified across 116 microbial sample runs using a library built from 64 standards.
  17. Se Pu. 2023 May 08. 41(5): 417-425
      Bisphenol A (BPA) is one of the most widely produced compounds in the world and was listed as a substance of very high concern by the European Chemicals Agency in 2016. Because of its toxicity, many countries and regions, including China, have banned BPA addition in feeding-bottles. And the European Union (EU) has banned BPA use in other food contact materials and thermal paper. Restrictions on BPA have contributed to the widespread use of alternatives. As the toxicity of BPA alternatives continues to be revealed, the alternatives of BPA alternatives are being developing. As the most extensive alternative for BPA, bisphenol S (BPS) was proven to have estrogen-disrupting effects and developmental toxicity of the neuroendocrine system. Therefore, BPS alternatives are used in thermal paper. In this study, alternatives to both BPA and BPS are collectively referred to as bisphenols (BPs). As a pooling matrix of many indoor chemicals, dust is an important pathway for human exposure to BPs. BPA and its alternatives are routinely detected in dust. As BPS alternatives have been detected in recycled paper and sludge, it is also very important to detected in dust. However, common analytical methods for BPs have low sensitivity and contain few BPS alternatives. Therefore, a high-throughput, high-accuracy, and high-sensitivity method must be established for the determination of BPs in dust; this will lay the foundation for subsequent studies on the environmental behavior and exposure risk of BPs. In this study, an ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed for the simultaneous determination of 26 variations of BPs in dust. UPLC-MS/MS parameters of the variations were optimized to compare the separation effect and response intensity in different columns and mobile phases. The influence of the extraction solvent and solid phase extraction (SPE) on the extraction efficiency and purification effect of target compounds were optimized by using the isotopic internal standard method, and the 26 variations of BPs in dust was quantitatively analyzed. Finally, the dust samples were extracted by using 3 mL of acetonitrile and 3 mL of a 50% methanol aqueous solution in an ultrasound bath. The combined extract was further purified by using an Oasis HLB cartridge (60 mg/3 mL). The cartridge was then washed with a 40% methanol aqueous solution (0.5 mL) and eluted with methanol (2 mL). The target compounds were separated on a CORTECS® UPLC® C18 column (100 mm×2.1 mm, 1.6 μm), with methanol and 1 mmol/L ammonium fluoride solution as mobile phases and a flow rate of 0.3 mL/min. Electrospray ionization (ESI) was applied in the positive, negative, and multiple reaction monitoring (MRM) modes for the mass scan. Under optimized conditions, the linear ranges of the 26 targets behaved well linearly in their respective ranges with correlation coefficients (r2)>0.999. The limits of detection (LODs) and limits of quantification (LOQs) were assessed using signal-to-noise (S/N) ratios of 3 and 10, respectively. The LODs and LOQs of the method were 0.01-0.75 μg/kg and 0.02-2.50 μg/kg, respectively. The accuracy of the method was evaluated by conducting a recovery test at three spiked levels: LOQ, two times the LOQ, and 10 times the LOQ, with the average recoveries ranging from 83.7% to 114.9%. The precision of the method was evaluated by using the relative standard deviation (RSD). The intra-day RSDs and inter-day RSDs were 0.86%-9.79% (n=6) and 5.16%-19.5% (n=6), respectively. The established method was used to determine 11 dust samples. Fifteen BPs were detected at a detection rate of 9.1%-100.0%. The detection rate for BPA, BPS, bisphenol F (BPF), 4-hydroxy-4'-isopropoxydiphenylsulfone (BPSIP), and diphenyl sulfone (DPS) was 100.0%. BPSIP, 4-allyloxy-4'-hydroxydiphenyl sulfone (BPS-MAE), and bis-(3-allyl-4-hydroxyphenyl) sulfone (TGSA) were first detected in Chinese dust, whereas 4-benzyloxy-4'-hydroxydiphenyl sulfone (BPS-MPE), 4-hydroxybenzoic acid benzyl (PHBB), and DPS were first detected in dust samples worldwide. This method is simple, rapid, and sensitive, and is suitable for the qualitative screening and quantitative analysis of the 26 BPs in dust samples.
    Keywords:  bisphenols (BPs); dust; ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  18. Methods Enzymol. 2023 ;pii: S0076-6879(22)00364-0. [Epub ahead of print]683 153-170
      Multi-omics has gained momentum over the past few years especially in plant single cell-type analysis as they aim to understand cellular molecular networks across different levels of genetic information flow. For multi-omics sample preparation, molecular extractions performed non-simultaneously create rooms for variation, inaccurate data, waste of limited samples, resources and labor. Here we optimized a protocol for 3-in-1 simultaneous extraction of RNA, metabolites, and proteins from the same single cell-type sample. We adapted a commercially available RNA kit with a few modifications to obtain high quality starting materials for sequencing and LC-MS/MS-based metabolomics and proteomics. RNAs are bound to the column, metabolites were extracted in a polar solvent and proteins are precipitated using acetone. This creates an all-in-one workflow using a standard RNA kit. Little training is required to carry out this protocol as it is simple and easy to use. It may be used with a wide range of plant species and different amounts of starting materials, including single cells.
    Keywords:  Arabidopsis thaliana; Guard cells; LC-MS/MS; Mesophyll cell protoplasts; Metabolomics; Multi-omics; Proteomics; Single cell-type
  19. ACS Biomater Sci Eng. 2023 Apr 24.
      The chemical characterization of extractables and leachables (E&Ls) is an important aspect of biosafety and biocompatibility assessment in medical device industry. The advent of the body-contact use of medical devices in patient treatment has introduced a potential source for extractables and leachables as these medical devices are comprised of various polymeric materials. Several industry working groups, the FDA and USP, have recognized the guidance for chemical characterizations and nontargeted analysis of medical device extracts, such as ISO 10993-18:2020. The MS application of nontargeted analysis has played a critical role in understanding the E&Ls from medical device extracts. However, there have been very few reports about the MS based workflow with nontargeted analysis for medical device extracts and there is little guidance about the exact methodologies which should be used, even though there is an urgent need for a clearly defined process for the identification of medical device extracts. In this study, we demonstrated an analytical LC/MS (liquid chromatography/mass spectrometry) workflow using high resolution Exploris120 Orbitrap instrument for data acquisition and Compound Discoverer 3.3 intelligent software for data processing to profile the polymer related E&Ls from a balloon dilation catheter device extracted with 40% ethanol. An E&L ID workflow combining LC separation, data-informed MS acquisition strategy, MS information mining (including adduct ions, MS information from both electrospray ionization (ESI) (+) and ESI (-), in-source fragmentation, common fragment ions (CFIs), common neutral losses (CNLs), and in silico MS simulation was described with intelligent software processing and manual data interpretation. The workflow developed in this study was proven to be effective to provide a comprehensive profile of polymer related degradation products, polymer impurities and additives including surfactants, UV curing agent, antioxidants, and plasticizers for the device analyzed. The classification of E&L compounds using CFIs and CNLs was very effective to facilitate the identification of polymer related impurities and extract the polymer related impurities with common structures in a large data result set.
    Keywords:  Chemical characterization; FISh; LC/MS; common fragment ion; common neutral loss; workflow
  20. Curr Protoc. 2023 Apr;3(4): e758
      Quantitative analysis of urine acylglycines has shown to be a highly sensitive and specific method with proven clinical utility for the diagnosis of several inherited metabolic disorders including: medium chain acyl-CoA dehydrogenase deficiency, multiple acyl-CoA dehydrogenase deficiency, short chain acyl-CoA dehydrogenase deficiency, 3-methylcrotonyl-CoA carboxylase deficiency, 2-methylbutyryl-CoA dehydrogenase deficiency, isovaleric acidemia, propionic academia, and isobutyryl-CoA dehydrogenase deficiency. Here, a method that is currently performed using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) is described. © 2023 Wiley Periodicals LLC. Basic Protocol: Urinary acylglycine analysis by UPLC-MS/MS Support Protocol 1: Quality control preparation Support Protocol 2: Internal standard (ISTD) preparation Support Protocol 3: Standard (STD)/calibrator preparation.
    Keywords:  UPLC-MS/MS; acylglycine; fatty acid β-oxidation; glycine N-acylase; organic acidemia
  21. J Mass Spectrom Adv Clin Lab. 2023 Apr;28 114-121
      Objectives: Recent studies have shown that derangements in kynurenine pathway metabolite levels are associated with various pathologies such as neurodegenerative diseases, schizophrenia, depression, bipolar disorder, rheumatoid arthritis, and cancer. Therefore, reliable, accurate, fast, and multiplex measurement methods for kynurenines have become increasingly important. This study aimed to validate a new mass spectrometric method for analyzing tryptophan metabolites.Methods: A tandem mass spectrometric method, including protein precipitation and evaporation steps, was developed to measure serum levels of tryptophan, kynurenine, kynurenic acid, 3-hydroxykynurenine, and 3-hydroxyanthranilic acid. Samples were separated using a Phenomenex Luna C18 reversed-phase column. The kynurenine pathway metabolites were detected by tandem mass spectrometry. The developed method was validated according to Clinical & Laboratory Standards Institute (CLSI) guidelines and applied to hemodialysis samples.
    Results: The developed method was linear at the concentrations of 48.8 - 25,000, 0.98 - 500, 1.2-5000, 1.2-5000, and 0.98-250 ng/mL for tryptophan, kynurenic acid, kynurenine, 3-hydroxyanthranilic acid, and 3-hydroxykynurenine, respectively. The imprecisions were less than 12 %. The median serum concentrations of tryptophan, kynurenine, kynurenic acid, 3-hydroxykynurenine, and 3-hydroxyanthranilic acid were 10530, 1100, 218, 17.6, and 25.4 ng/mL in pre-dialysis blood samples, respectively. They were 4560, 664, 135, 7.4, and 12.8 ng/mL in post-dialysis blood samples, respectively.
    Conclusions: A fast, simple, cost-effective, accurate, robust, and validated tandem mass spectrometric method was developed, and the method was successfully used for the quantitation of kynurenine pathway metabolite concentrations in hemodialysis patients.
    Keywords:  Kynurenine pathway; Mass spectrometry; Tryptophan; Validation
  22. Anal Chem. 2023 Apr 27.
      A high-throughput droplet imbibition mass spectrometry (MS) experiment is reported for the first time that allows direct analysis of ultra-small volumes of complex mixtures. In this experiment, an array of optimized tips of glass capillaries containing the analyte solution is sampled by rapidly moving charged microdroplets, which picks up (i.e., imbibes) the analyte and transfers it to a proximal mass spectrometer. The advantages associated with this droplet imbibition experiment include (1) ultra-small sample consumption (1.3 nL/min), which reduces the matrix effect in complex mixture analysis, and (2) high surface activity, which eliminates ion suppression effects caused by competition for the space charge on the droplet surface. Collectively, the enhanced surface effect and small flow rates dramatically increase the sensitivity of the droplet imbibition MS approach. This was experimentally shown by constructing calibration curves for cocaine analysis in human raw urine and whole blood, achieving 2 and 7 pg/mL limits of detection, respectively. The high-throughput feature was demonstrated by analyzing five structurally different compounds in 20 s intervals. With the measured flow rate of 1.3 nL/min on a 5 μm glass tip size, the results described in the current study showcase droplet imbibition MS to be a powerful and high-throughput alternative for conventional nano-electrospray ionization (flow rate <100 nL/min), which is the most efficient method for transferring small sample volumes to mass spectrometers.
  23. Metabolites. 2023 Apr 13. pii: 558. [Epub ahead of print]13(4):
      High-throughput metabolomics has enabled the development of large-scale cohort studies. Long-term studies require multiple batch-based measurements, which require sophisticated quality control (QC) to eliminate unexpected bias to obtain biologically meaningful quantified metabolomic profiles. Liquid chromatography-mass spectrometry was used to analyze 10,833 samples in 279 batch measurements. The quantified profile included 147 lipids including acylcarnitine, fatty acids, glucosylceramide, lactosylceramide, lysophosphatidic acid, and progesterone. Each batch included 40 samples, and 5 QC samples were measured for 10 samples of each. The quantified data from the QC samples were used to normalize the quantified profiles of the sample data. The intra- and inter-batch median coefficients of variation (CV) among the 147 lipids were 44.3% and 20.8%, respectively. After normalization, the CV values decreased by 42.0% and 14.7%, respectively. The effect of this normalization on the subsequent analyses was also evaluated. The demonstrated analyses will contribute to obtaining unbiased, quantified data for large-scale metabolomics.
    Keywords:  cohort study; lipid; liquid chromatography–mass spectrometry; quality control; targeted lipidomics
  24. Rapid Commun Mass Spectrom. 2023 Apr 27. e9528
      RATIONALE: Microbial metabolites are widely used in agriculture, food, environment, and medicine. However, there is a lack of high-throughput, non-clogging, and simple methods for the identification of microbial metabolites and their subspecies using ambient mass spectrometry. Herein, we proposed a method for analyzing the microbial metabolites and identifying their species using the array ballpoint electrospray ionization (aBPESI) technique.METHODS: The previously developed ballpoint electrospray ionization (BPESI) was combined with the array analysis technique to form a high-throughput analysis technique, aBPESI. The bacteria cultured on the plate medium are directly analyzed by mass spectrometry with aBPESI. PCA-LDA algorithm was used to analyze different subspecies groups.
    RESULTS: The results showed that aBPESI was capable of completing the analysis of a sample within 30 s, and the level of metabolite detection was comparable to existing techniques. The accuracy of bacterial subspecies identification was 90% (Pseudomonas aeruginosa) and 100% (Serratia marcescens), respectively.
    CONCLUSIONS: A new high throughput and robust mass spectrometry technique aBPESI was proposed. It does not require sample pretreatment and greatly shortens the sample analysis time. aBPESI shows a strong ability in microbial analysis and is expected to be further applied in other research fields.
  25. Biomed Chromatogr. 2023 Apr 28. e5664
      In this study, the development and validation of an accurate and highly sensitive LC-MS/MS method were performed for the estimation of nifedipine, bisoprolol, and captopril in real human plasma. Liquid-liquid extraction using tert-butyl methyl ether was efficiently applied for extraction of the analytes from plasma samples. The chromatographic separation was carried out using an isocratic elution mode on the X-terra MS C18 column (4.6 × 50 mm, 3.5 μm). The mobile phase consisted of methanol: 0.1 % formic acid (95:5, v/v) for determination of nifedipine and bisoprolol and acetonitrile: 0.1 % formic acid (70:30, v/v) for determination of captopril with a flow rate of 0.5 mL/min. Acceptable results regarding the different validation characteristics of the analytes were obtained in accordance with US-FDA recommendations for bioanalytical methods. The developed approach was linear over concentration ranges of 0.5-130.0, 50.0-4500.0, and 0.3-30.0 ng/mL for nifedipine, captopril, and bisoprolol, respectively. The method revealed a sufficient lower limit of quantification (LLOQ) in the range of 0.3-50.0 ng/mL, as well as high recovery percentages, indicating high bioanalytical applicability. The proposed method was efficiently applied to a pharmacokinetic evaluation of a fixed-dose combination of the analytes in healthy male volunteers.
    Keywords:  Bisoprolol; Captopril; Human plasma; LC-MS/MS; Nifedipine; Pharmacokinetic study