bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2023‒06‒04
28 papers selected by
Sofia Costa

  1. Se Pu. 2023 Jun 08. 41(6): 520-526
      Gas chromatography-mass spectrometry (GC-MS) detectors are widely used detection instruments owing to their distinct advantages over other analytical techniques, including lower sample consumption, higher sensitivity, faster analysis speed, and simultaneous separation and analysis. Metabolomics is an important component of system physiology that concerns systematic studies of the metabolite spectrum in one or more biological systems, such as cells, tissues, organs, body fluids, and organisms. Unfortunately, conventional GC-MS detectors also feature low scan rates, high ion loss rates, and a narrow concentration detection range, which limit their applications in the field of metabolomics. Therefore, establishing a GC-MS-based metabolomic analysis method with wide coverage is of great importance. In this research, a widely-targeted metabolomics method based on GC-MS is proposed. This method combines the universality of untargeted metabolomics with the accuracy of targeted metabolomics to realize the qualitative and semi-quantitative detection of numerous metabolites. It does not require a self-built database and exhibits high sensitivity, good repeatability, and strong support for a wide range of metabolic substances. The proposed method was used to establish the relationship between the retention time of straight-chain fatty acid methyl esters (FAMEs) and their retention index (RI) in the FiehnLib database based on the metabolite information stored in this database. We obtained a linear relationship that could be described by the equation y=40878x-47530, r2=0.9999. We then calculated the retention times of metabolites in the FiehnLib database under the experimental conditions based on their RI. In this way, the effects of significant variations in peak retention times owing to differences in the chromatographic column, temperature, carrier gas flow rate, and so on can be avoided. The retention time of a substance fluctuates within a certain threshold because of variations in instrument performance, matrix interference, and other factors. As such, the retention time threshold of the substance must be determined. In this paper, the retention time threshold was set to 0.15 min to avoid instrument fluctuations. The optimal scan interval was optimized to 0.20 s (possible values=0.10, 0.15, 0.20, 0.25, and 0.30 s) because longer sampling periods can lead to spectral data loss and reductions in the resolution of adjacent chromatographic peaks, whereas shorter sampling periods can result in deterioration of the signal-to-noise ratio of the collected signals. The metabolite quantification ions were optimized to avoid the interference of quantification ion peak accumulation in the case of similar peak times, and a selected ion monitoring (SIM) method table was constructed for 611 metabolites, covering 65% of the metabolic pathways in the KEGG (Kyoto Encyclopedia of Genes and Genomes). The developed method covered 39 pathways, including glycolysis, the tricarboxylic acid cycle, purine metabolism, pyrimidine metabolism, amino acid metabolism, and biosynthesis. Compared with the full-scan untargeted GC-MS method, the widely-targeted GC-MS method demonstrated a 20%-30% increase in the number of metabolites detected, as well as a 15%-20% increase in signal-to-noise ratio. The results of stability tests showed that 84% of the intraday relative standard deviations (RSDs) of metabolite retention times were less than 2% and 91% of that were less than 3%; moreover, 54% of the interday RSDs of metabolite retention times were less than 2% and 76% of that were less than 3%. The detection and analysis results of common biological samples confirmed that the proposed method greatly improved the quantity and signal-to-noise ratio of the detected metabolites and is applicable to substances that are thermally stable, volatile, or volatile after derivation and have relative molecular masses lower than 600. Thus, the widely-targeted GC-MS method can expand the application scope of GC-MS in metabolomics.
    Keywords:  gas chromatography-mass spectrometry (GC-MS); metabolic pathway; metabolomics; method development; widely-targeted
  2. Methods Mol Biol. 2023 ;2675 65-76
      Quantification of amino acids in biological samples is a critical tool for studying metabolism. Although many methods for amino acid analysis exist, important considerations include ease of sample preparation, dynamic range, reproducibility, instrument availability, and throughput. Here, we present a simple, rapid, and robust method for the analysis of amino acids by chemical derivatization and liquid chromatography-mass spectrometry (LC-MS). We provide a detailed protocol for the analysis of 20 proteinogenic amino acids in biological samples which will enable straightforward implementation on modern LC-MS instruments.
    Keywords:  Amino acid analysis; Dansylation; Liquid chromatography-mass spectrometry
  3. J Chromatogr A. 2023 May 26. pii: S0021-9673(23)00337-0. [Epub ahead of print]1703 464111
      Branched chain fatty acids (BCFAs) are one of the important sub categories of fatty acids (FAs) which have unique functions in nature. They are commonly analyzed by GC-MS after derivatization to methyl esters (FAMEs). On the other hand, there is a lack of isomer-selective LC-MS methods which allow the distinction of different isomers with wide coverage of carbon chain length. In this work, a systematic retention and isomer selectivity study on seven commercially available UHPLC columns (six polysaccharide columns Chiralpak IA-U, IB-U, IC-U, ID-U, IG-U and IH-U; one Acquity UPLC CSH C18 column) was performed. Various experimental factors were evaluated including column temperatures, gradient profiles and flow rates to elucidate their effects on the separation ability of homologous series of BCFAs with distinct chain lengths, different branching types and branching positions. In general, IG-U outperformed the other columns in terms of isomer selectivity especially for the short and medium-chain BCFA isomers while RP C18 showed good potential in terms of selectivity for long-chain BCFA isomers. Furthermore, after the evaluation of the chromatographic retention pattern on the various columns and method optimization, we report a methodology for untargeted isomer-selective BCFA profiling without precolumn derivatization with UHPLC-ESI-MS/MS by quadrupole-time-of-flight instrument with SWATH acquisition. The best method provides selectivity for constitutional isomers of BCFAs covering distinct chain length (C5-C20) with different branching types (methyl or ethyl) and branching positions (2Me, 3Me, 4Me, 6Me, anteiso and iso-BCFAs) with an optimized LC condition on Acquity UPLC CSH C18 column. Finally, the optimized method was applied for the BCFAs profiling in lipid extracts of Staphylococcus aureus samples. Besides, pooled human platelets and pooled human plasma were evaluated as mammalian samples for presence of BCFAs as well. The new method showed strong potential for BCFA profiling in bacterial samples including different isomers anteiso and iso-BCFAs, which could be a useful tool for related subdisciplines in metabolomics and lipidomics in particular in combination with electron-activated dissociation MS. Compared to GC, the presented isomer selective LC methods can be also of great utility for preparative purposes. Equivalent (carbon) chain length numbers were calculated for RP18 and Chiralpak IG-U and compared to those of FAMEs obtained by GC.
    Keywords:  Bacterial fatty acids; Isomer; Lipidomics; Microbiome; Staphylococcus aureus
  4. Se Pu. 2023 Jun 08. 41(6): 497-503
      Fluoroacetic acid is a highly polar poison used for rodent control. When ingested by the human body, it seriously damages nerve cells and heart tissues and even causes death by cardiac arrest or respiratory failure. Common detection methods for fluoroacetic acid include gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry, both of which require complex pretreatment methods, such as derivatization. In this study, a method to determine fluoroacetic acid in human blood and urine based on accelerated solvent extraction-ion chromatography-mass spectrometry (ASE-IC-MS) was established. Two pretreatment methods, namely, acetonitrile precipitation and accelerated solvent extraction, were compared. Furthermore, the effects of different extraction conditions, such as the extraction time, extraction temperature, and number of cycles, were investigated. The most suitable chromatographic separation conditions, such as the chromatographic column, column temperature, and elution procedure, were determined, and the MS conditions, such as the collision energy (CE) and declustering potential (DP) of the ion pairs of the target compound, were investigated. Based on the experimental results, the optimal pretreatment methods and detection conditions were obtained, and reliable data were collected. Deionized water was used as the extraction solvent, and blood and urine samples were processed by accelerated solvent extractor. The supernatant was sequentially collected via centrifugal ultrafiltration and 0.22 μm membrane filtration, diluted 50 times, and then injected into the chromatographic column for detection. An Ion Pac AS20 IC column was used for isocratic elution with 15.0 mmol/L KOH solution as the eluent. The effluent was passed through a suppressor and into a triple quadrupole mass spectrometer, which was used to perform MS/MS (ESI-) in multiple reaction monitoring (MRM) mode. The quantitative ion was m/z 77.0>57.0 when the CE and DP were -15.0 eV and -20.0 V, respectively. An external standard method was used for quantitative analysis. The results showed a good linear relationship for fluoroacetic acid in the range of 0.5-500.0 μg/L (r>0.999), with limits of detection (LOD) and quantification (LOQ) of 0.14 and 0.47 μg/L, respectively. The recoveries of fluoroacetic acid in blood and urine were 93.4%-95.8% and 96.2%-98.4%, respectively. The intra-day RSDs for blood and urine were 0.8%-1.6% and 0.2%-1.0%, respectively, while the inter-day RSDs were 2.3%-3.8% and 3.9%-6.9%, respectively. Further investigation revealed that the matrix effects of this method in blood and urine, at -7.4% and -3.0%, respectively, were fairly weak. The established method was successfully applied to detect fluoroacetic acid in human blood and urine obtained from a poisoning case, and the results obtained provided crucial clues that led to swift case resolution. The efficiency of the method was significantly higher than that of conventional detection methods. In conclusion, the developed method has high sensitivity and good repeatability and is suitable for the rapid detection of fluoroacetic acid in human blood and urine. Moreover, because this method does not require derivatization, it is simple and efficient.
    Keywords:  accelerated solvent extraction (ASE); blood; centrifugal ultrafiltration; fluoroacetic acid; ion chromatography-tandem mass spectrometry (IC-MS/MS); urine
  5. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2023 May 20. 41(5): 366-371
      Objective: To establish ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method for the determination of 22 phospholipids in serum. Methods: In September 2022, Using synthetic non endogenous phospholipids as internal standard, phospholipids in serum were extracted by methanol-dichloromethane (2∶1, V/V) protein precipitation method. Chromatographic separation was achieved on an ACQUITY UPLC BEH shield RP18 column, and the mobile phase was methanol/water (5∶95, V/V) containing 10 mM ammonium formate and methanol. Detection was performed in multiple reaction monitoring mode with ion mode switching. And the method was applied by analyzing phospholipids in the serum of coal workers' pneumoconiosis patients. Results: The 22 phospholipids showed good linear relationships in their respective concentration ranges and the correlation coefficients were higher than 0.990. The spiked recoveries of the 22 phospholipids were 81.03%-121.63% at the three spiked levels. The intra-assay were less than 14.52%, and the inter-assay were less than 15.00%. Conclusion: The method with the advantages of simplicity, stability and high sensitivity, and it can be used for the analysis of phospholipids in serum.
    Keywords:  Liquid chromatography-tandem mass spectrometry (LC-MS/MS); Phospholipids; Serum
  6. Anal Chim Acta. 2023 Jul 25. pii: S0003-2670(23)00529-9. [Epub ahead of print]1266 341308
      Data-dependent acquisition (DDA) is the most widely used mode in untargeted metabolomic analysis despite its limited tandem mass spectrometry (MS2) detection coverage. We present MetaboMSDIA for complete processing of data-independent acquisition (DIA) files by the extraction of multiplexed MS2 spectra and further identification of metabolites in open libraries. In the analysis of polar extracts from lemon and olive fruits, DIA allows one to obtain multiplexed MS2 spectra for 100% of precursor ions compared to 64% of precursor ions from average MS2 acquisition in DDA. MetaboMSDIA is compatible with MS2 repositories and homemade libraries prepared by analysis of standards. An additional option is based on filtering molecular entities by searching for selective fragmentation patterns according to selective neutral losses or product ions to target the annotation of families of metabolites. Combining both options, the applicability of MetaboMSDIA was tested by annotating 50 and 35 metabolites in polar extracts from lemon and olive fruit, respectively. MetaboMSDIA is particularly proposed to increase the acquisition coverage in untargeted metabolomics and to improve spectral quality, which are two critical pillars for the tentative annotation of metabolites. The R script used in MetaboMSDIA workflow is available at github repository (
    Keywords:  Data-independent acquisition; Mass spectrometry; Multiplexed MS2 spectra; R package; metabolites annotation
  7. Bioinformatics. 2023 May 30. pii: btad354. [Epub ahead of print]
      MOTIVATION: Tandem mass spectrometry is an essential technology for characterizing chemical compounds at high sensitivity and throughput, and is commonly adopted in many fields. However, computational methods for automated compound identification from their MS/MS spectra are still limited, especially for novel compounds that have not been previously characterized. In recent years, in silico methods were proposed to predict the MS/MS spectra of compounds, which can then be used to expand the reference spectral libraries for compound identification. However, these methods did not consider the compounds' three-dimensional (3D) conformations, and thus neglected critical structural information.RESULTS: We present the 3D Molecular Network for Mass Spectra Prediction (3DMolMS), a deep neural network model to predict the MS/MS spectra of compounds from their 3D conformations. We evaluated the model on the experimental spectra collected in several spectral libraries. The results showed that 3DMolMS predicted the spectra with the average cosine similarity of 0.691 and 0.478 with the experimental MS/MS spectra acquired in positive and negative ion modes, respectively. Furthermore, 3DMolMS model can be generalized to the prediction of MS/MS spectra acquired by different labs on different instruments through minor fine-tuning on a small set of spectra. Finally, we demonstrate that the molecular representation learned by 3DMolMS from MS/MS spectra prediction can be adapted to enhance the prediction of chemical properties such as the elution time (ET) in the liquid chromatography and the collisional cross section (CCS) measured by ion mobility spectrometry (IMS), both of which are often used to improve compound identification.
    AVAILABILITY: The codes of 3DMolMS are available at and the web service is at
  8. Se Pu. 2023 Jun 08. 41(6): 490-496
      Halobenzoquinones (HBQs), which are emerging chlorinated disinfection byproducts (DBPs), have attracted increasing attention because they are frequently detected in treated tap water, entrainment water, etc. These compounds are mainly generated during the water treatment process using chlorine, chloramine, and chlorine dioxide as disinfectants, and display more toxic effects than regulated DBPs, such as trihalomethane and haloacetic acid. HBQs have been recognized as potential bladder carcinogens and are harmful to the nervous system. Additionally, they can exert genotoxic effects and cause oxidative damage to DNA and proteins. The risk of HBQs in aquatic products is expected to rise because the disinfection of public facilities has significantly increased in recent years. Therefore, developing a sensitive and accurate analytical method to detect HBQs in aquatic products is of great importance. Several analytical methods, including gas chromatography, gas chromatography-mass spectrometry, electrochemical methods, liquid chromatography, and liquid chromatography-tandem mass spectrometry, can be used to identify and quantify HBQs in water. However, to the best of our knowledge, no reports on the determination of HBQ levels in aquatic products are yet available. Further, pretreatment is essential for HBQ determination because of the complex matrix effects of aquatic products. Herein, a sensitive and accurate method based on the QuEChERS technique coupled with ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed for the simultaneous determination of five HBQs in aquatic products. For the QuEChERS procedure, the pretreatment conditions, such as the extraction solvent and adsorbent species, were systematically optimized. The sample was extracted with 10 mL of 10% methanol acetonitrile solution (containing 0.1% formic acid), dehydrated, and centrifuged with sodium chloride and anhydrous magnesium sulfate. The supernatant was purified using a QuEChERS packing material consisting of 50 mg N-propylethylenediamine (PSA), 30 mg of graphitized carbon black (GCB), and 30 mg of neutral alumina (Al2O3), dried with nitrogen, and concentrated. The five HBQs were separated on a Waters ACQUITY UPLC BEH C18 column (100 mm×2.1 mm, 1.7 μm) using 0.25% acetonitrile formate solution and 0.25% formic acid aqueous solution as the mobile phase under a gradient elution program and then detected using UPLC-MS/MS with negative electrospray ionization (ESI-) under multiple reaction monitoring (MRM) mode. Quantitative analysis was performed using a matrix-matched external standard method. The five HBQs achieved rapid separation within 6 min, indicating that the proposed method has a much shorter separation time compared with previous studies. The matrix effect was evaluated by establishing a matrix-matched calibration curve. The results showed that 2,5-dichloro-1,4-benzoquinone (2,5-DCBQ) presented a matrix-enhancing effect, whereas the other HBQs displayed matrix-inhibiting effects. In particular, tetrachlorobenzoquinone (TCBQ) exhibited strong inhibitory effects. Under the optimized experimental conditions, the five HBQs demonstrated good linear relationships in the range of 1.0-50.0 μg/L, with correlation coefficients (r)≥0.9992. The detection limits of the method were 0.15-0.8 μg/kg, and the recoveries of the target compounds were 85.9%-116.5%. The relative standard deviations were 1.4%-8.2%, which indicates good reproducibility. The proposed method was successfully applied to actual sample detection, and 2,6-dichloro-3-methyl-1,4-benzoquinone (2,6-DCMBQ) was detected in grass carp. The proposed method is convenient, sensitive, accurate, and suitable for the simultaneous determination of five HBQs in aquatic products. Moreover, the developed method provides a reliable reference for the routine monitoring of trace HBQs in food samples.
    Keywords:  QuEChERS; aquatic products; halobenzoquinones (HBQs); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  9. iScience. 2023 Jun 16. 26(6): 106881
      Mass spectrometry (MS)-based untargeted metabolomic and lipidomic approaches are being used increasingly in biomedical research. The adoption and integration of these data are critical to the overall multi-omic toolkit. Recently, a sample extraction method called Multi-ABLE has been developed, which enables concurrent generation of proteomic and untargeted metabolomic and lipidomic data from a small amount of tissue. The proteomics field has a well-established set of software for processing of acquired data; however, there is a lack of a unified, off-the-shelf, ready-to-use bioinformatics pipeline that can take advantage of and prepare concurrently generated metabolomic and lipidomic data for joint downstream analyses. Here we present an R pipeline called MultiABLER as a unified and simple upstream processing and analysis pipeline for both metabolomics and lipidomics datasets acquired using liquid chromatography-tandem mass spectrometry. The code is available via an open-source license at
    Keywords:  Biological sciences research methodologies; Biological sciences tools; Lipidomics; Metabolomics
  10. Anal Chem. 2023 Jun 01.
      Untargeted metabolomics is a powerful tool for investigating chemistry of complex biological systems, but its utility is compromised by the presence of uninformative features and the limited efficiency of currently available prioritization tools. More effective filtering and prioritization tools are required to address the challenges of large untargeted metabolomics datasets. Here, we introduce Metabolomics Peak Analysis Computational Tool (MPACT), a new mass spectrometry data analysis platform employing filtering based on multiple modalities, statistical techniques incorporating multilevel replication, and interactive data visualization. We demonstrate application of MPACT to uncover hidden effects of the rare earth element cerium on tunicate-associated bacterium Streptomyces sp. PTY087I2, culminating in characterization of two thiolated compounds including a new cysteine derivative, granaticin C, and granaticin D, recently described as mycothiogranaticin A. While we demonstrate application of MPACT to microbial natural products discovery using an elicitation approach, the platform should be readily adaptable to investigation of multipartite interactions, biomarker detection, small molecules in the environment, and a wide range of other complex sample types.
  11. Anal Chem. 2023 Jun 01.
      Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an m/z selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist. Quantum-chemically computed spectra can reliably be used as reference, but the challenge of selecting the candidate structures remains. Here, we introduce an in silico library of vibrational spectra of common MS adducts of over 4500 compounds found in the human metabolome database. In total, the library currently contains more than 75,000 spectra computed at the DFT level that can be queried with an experimental IR spectrum. Moreover, we introduce a database of 189 experimental IRIS spectra, which is employed to validate the automated spectral matching routines. This demonstrates that 75% of the metabolites in the experimental data set are correctly identified, based solely on their exact m/z and IRIS spectrum. Additionally, we demonstrate an approach for specifically identifying substructures by performing a search without m/z constraints to find structural analogues. Such an unsupervised search paves the way toward the de novo identification of unknowns that are absent in spectral libraries. We apply the in silico spectral library to identify an unknown in a plasma sample as 3-hydroxyhexanoic acid, highlighting the potential of the method.
  12. Methods Mol Biol. 2023 ;2675 133-148
      Oxidation of glutathione (GSH) to its disulfide dimer (GSSG) is the major mechanism by which cells balance reactive oxygen species (ROS) and mitigate oxidative stress. Thus, measuring the ratio of GSH/GSSG is an ideal way to assess oxidative stress within a cell. Quantitative mass spectrometry offers an ideal method to measure the GSH/GSSG ratio and can be applied to a variety of biological matrices and disease models. The following chapter details the design, optimization, and execution of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay to measure the GSH/GSSG ratio.
    Keywords:  Glutathione; Liquid chromatography; Mass spectrometry; Oxidative stress; Oxidized glutathione; Quantitation; Reactive oxygen species
  13. Anal Chem. 2023 Jun 01.
      Nitric oxide (NO) is a highly reactive signaling molecule involved in diverse biological processes. Simultaneous profiling of NO and associated metabolic fingerprints in a single assay allows more accurate assessments of cell states and offers the possibility to better understand its exact biological roles. Herein, a multiplexing LC-MS workflow was established for simultaneous detection of intracellular NO and various metabolites based on a novel "iridium signature" mass spectrometric probe (Ir-MSP841). This Ir-MSP841 can convert highly liable NO to a stable permanently charged triazole product (Ir-TP852), enabling direct MS detection of NO. This 191/193Ir-signature mass spectrometric probe-based approach is endowed with overwhelming advantages of interference-free, high quantitative accuracy, and great sensitivity (limit of detection down to 0.14 nM). It also reveals good linearity over a wide concentration range 12.5-500 nM and has been successfully employed for exploring the release behaviors of three representative NO donors in cells. Meanwhile, metabolic profiling results reveal that varying the concentrations of NO has distinct effects on various cellular metabolites. This study provides a robust, sensitive, and versatile method for simultaneous detection of NO and numerous metabolites in a single LC-MS run and expands its applications in biomedical research.
  14. Magn Reson Chem. 2023 Jun 02.
      Nuclear magnetic resonance (NMR) spectral analysis of biofluids can be a time-consuming process, requiring the expertise of a trained operator. With NMR becoming increasingly popular in the field of metabolomics, there is a growing need to change this paradigm and to automate the process. Here we introduce MagMet, an online web server, that automates the processing and quantification of 1D 1 H NMR spectra from biofluids-specifically, human serum/plasma metabolites, including those associated with inborn errors of metabolism (IEM). MagMet uses a highly efficient data processing procedure that performs automatic Fourier Transformation, phase correction, baseline optimization, chemical shift referencing, water signal removal, and peak picking/peak alignment. MagMet then uses the peak positions, linewidth information, and J-couplings from its own specially prepared standard metabolite reference spectral NMR library of 85 serum/plasma compounds to identify and quantify compounds from experimentally acquired NMR spectra of serum/plasma. MagMet employs linewidth adjustment for more consistent quantification of metabolites from higher field instruments and incorporates a highly efficient data processing procedure for more rapid and accurate detection and quantification of metabolites. This optimized algorithm allows the MagMet webserver to quickly detect and quantify 58 serum/plasma metabolites in 2.6 min per spectrum (when processing a dataset of 50-100 spectra). MagMet's performance was also assessed using spectra collected from defined mixtures (simulating other biofluids), with >100 previously measured plasma spectra, and from spiked serum/plasma samples simulating known IEMs. In all cases, MagMet performed with precision and accuracy matching the performance of human spectral profiling experts. MagMet is available at
    Keywords:  1H NMR; automation; metabolite identification; metabolite quantification; software
  15. Methods Mol Biol. 2023 ;2669 67-77
      Retinoids are light-sensitive molecules that are normally detected by UV absorption techniques. Here we describe the identification and quantification of retinyl ester species by high-resolution mass spectrometry. Retinyl esters are extracted by the method of Bligh and Dyer and subsequently separated by HPLC in runs of 40 min. The retinyl esters are identified and quantified by mass spectrometry analysis. This procedure enables the highly sensitive detection and characterization of retinyl esters in biological samples such as hepatic stellate cells.
    Keywords:  Atmospheric pressure chemical ionization; High-performance liquid chromatography; Mass spectrometry; Orbitrap; Retinol; Retinyl esters; Vitamin A
  16. J Chromatogr A. 2023 May 20. pii: S0021-9673(23)00312-6. [Epub ahead of print]1702 464086
      Liquid chromatography with tandem mass spectrometry (LC-MS/MS) is the golden standard for immunosuppressants analyses, where optimising throughput by parallel chromatography can reduce costs and turnaround time. We aimed to double our system throughput using a dual LC-MS/MS setup. Therefore, two independent UPLC systems were hyphenated to one triple quadrupole MS, with staggered injections from one autosampler on alternating columns. The method simultaneously measured the analytes tacrolimus, sirolimus, everolimus, and cyclosporin A in whole blood using isotope dilution, with a run time of 1.5 min. Using the dual LC-MS/MS system, net run-to-run time improved from 2.3 to 0.98 min per injection, where throughput increased from 26 to 61 injections per hour. For Performance Qualification, 1101 clinical samples were measured on the dual LC-MS/MS system in addition to the standard system, during a period of one month, and the results were compared using Passing Bablok regression and Bland Altman analysis. There was excellent agreement for all four analytes, with regression slopes of 0.98-1.02x and intercepts of -0.11-0.88 µg/L. Minor bias was demonstrated between the systems with mean differences from -0.93 to 1.43%. In conclusion, the throughput was doubled and idle MS time was reduced with good agreement to the standard system. Currently, the method is applied for clinical routine with frequent peak intensities of >180 injections per day.
    Keywords:  Dual LC MS MS; Dual channel chromatography; Optimal MS MS utilisation; Productivity optimisation; Ultrahigh-speed
  17. J Lipid Res. 2023 May 29. pii: S0022-2275(23)00066-4. [Epub ahead of print] 100393
      Odd chain fatty acids (OCFAs) present in very low level at nearly 1% of total fatty acids in human plasma and thus their functions were usually ignored. Recent epidemiological studies have shown that OCFAs are inversely associated with a variety of disease risks. However, the contribution of OCFAs incorporated into complex lipids remains elusive. Here, we developed a targeted odd chain fatty acyl containing lipidomics method based on equivalent carbon number and retention time prediction. The method displayed good reproducibility and robustness as shown by peak width at half height within 0.7 min and coefficient of variation (CV) under 20%. A total number of 776 lipid species with odd chain fatty acyl residues could be detected in the electrospray ionization (ESI) mode of reverse phase liquid chromatography-mass spectrometry, of which 309 lipids were further validated using multiple MRM transitiions. Using this method, we quantified odd chain fatty acyl containing lipidome in tissues from 12 colon cancer patients, revealing the remodeling of triacylglycerol (TAG). The dynamics of odd chain fatty acyl lipids were further consolidated by the association with genomic and proteomic feature of altered catabolism of branched chain amino acids and TAG endogenous synthesis in colon cancer. This lipidomics approach will be applicable for screening of dysregulated odd chain fatty acyl lipids, which enriches and improves the methods for diagnosis and prognosis evaluation of cancer using lipidomics.
    Keywords:  Odd chain fatty acids; colon cancer; equivalent carbon number; lipidomics; liquid chromatography-mass spectrometry
  18. Methods Mol Biol. 2023 ;2675 51-63
      The analysis of metabolic perturbation in biological samples is crucial to understand mechanisms of metabolic diseases. Here, we describe a protocol for quantitative stable isotope-labeled metabolite tracing of cysteine metabolism in cultured cells. This protocol relies on an extraction protocol to derivatize free thiols to prevent oxidation. In addition, the quantitative tracing of serine into multiple pathways, including the glutathione synthesis pathway, allows for the interrogation of cysteine and glutathione synthesis. This protocol provides a flexible framework that can be adapted to interrogate many metabolites and pathways of interest.
    Keywords:  Cell culture; Cysteine; Mass spectrometry; Quantification; Serine; Stable isotope standard; Stable isotope tracing
  19. Anal Bioanal Chem. 2023 Jun 01.
      The lipid membrane is gaining appreciation as a critical factor in the emergence of antibiotic resistance, both for antibiotics that target lipid synthesis or the membrane directly and for cell-wall-targeting antibiotics. The methods used to study the emergence of antibiotic resistance in vitro can generate a large number of samples that may be low in volume and in cell density. As in eukaryotic/mammalian lipidomics, two-phase liquid-liquid extractions are the most commonly used approach to recover lipids from bacteria. The need to separate the lipid layer is cumbersome for high-throughput applications and can be a source of poor reproducibility or contaminant introduction. While several single-phase extractions have been proposed for serum, tissue, and eukaryotic cells, there have been far fewer efforts to adapt or develop such methods for bacteria lipidomics. Here, we describe a simple, single-phase lipid extraction method based on methanol, acetonitrile, and water-the MAW method. The merits of the MAW method are evaluated against the Bligh & Dyer (B&D) method for the recovery of the major membrane lipids (phosphatidylglycerols, diglycosyldiacylglycerols, and lysyl-phosphatidylglycerols) in the Gram-positive pathogen Staphylococcus aureus. We demonstrate that the MAW method achieves recoveries that are comparable to that of the B&D extraction (≥ 85% for PG 15:0/d7-18:1). The benefits of the MAW method enable the detection of lipids from lower amounts of bacteria than the B&D method (0.57 vs 0.74 McFarlands for PG 32:0, respectively) and is easily scaled down to microplate volumes to facilitate high-throughput studies of bacterial lipids.
    Keywords:  Bacteria; Extraction; High-throughput; Lipids; Single-phase; Staphylococcus aureus
  20. Methods Mol Biol. 2023 ;2675 181-194
      Feeding of stable 13C-labeled compounds coupled to mass spectrometric analysis has enabled the characterization of dynamic metabolite partitioning in various experimental conditions. This information is particularly relevant for the study and functional understanding of brain metabolic heterogeneity. We here describe a protocol for the analysis of metabolic enrichment analysis upon feeding of murine acute cerebellar slices with 13C-labeled substrates.
    Keywords:  13C labeling; Brain slices; Cellular metabolism; Cerebellum; Isotope enrichment; Liquid chromatography; Mass spectrometry
  21. J Chromatogr B Analyt Technol Biomed Life Sci. 2023 May 19. pii: S1570-0232(23)00168-X. [Epub ahead of print]1224 123758
      Raffinose and planteose are non-reducing, isomeric trisaccharides present in many higher plants. Structurally, they differ in the linkage of α-D-galactopyranosyl to either glucose C(6) or to C (6') of fructose, respectively and thus differentiating each other is very challenging. The negative ion mode mass spectrometric analysis is shown to distinguish planteose and raffinose. However, to facilitate the robust identification of planteose in complex mixtures, herein, we have demonstrated the use of porous graphitic carbon (PGC) chromatography combined with QTOF-MS2 analysis. The separation of planteose and raffinose was achieved on PGC, wherein both have recorded different retention time. Detection through MS2 analysis revealed the specific fragmentation patterns for planteose and raffinose that are distinctive to each other. The applicability of this method on oligosaccharides pool extracted from different seeds showed clear separation of planteose that allowed unambiguous identification from complex mixtures. Therefore, we propose PGC-LC-MS/MS can be employed for sensitive, throughput screening of planteose from wider plant sources.
    Keywords:  Mass spectrometry; Negative mode; Planteose; Porous graphitic carbon; Raffinose
  22. Se Pu. 2023 Jun 08. 41(6): 482-489
      Disinfection of drinking water is critical to prevent waterborne diseases. An unexpected consequence of water disinfection is the formation of disinfection by-products by the interaction of disinfectants with organic matter (natural or anthropogenic) and halides, which present significant toxicological effects and carcinogenic risks. As an emerging disinfection by-product, halobenzoquinones (HBQs) have attracted increasing attention owing to their severe toxicity and high detection rates. The credible determination of HBQs is essential for further studies on their occurrence, toxicity, and control measures; however, HBQs are usually detected in drinking water at trace levels. Therefore, accurate and efficient analytical techniques are critical for HBQ determination and quantitation. In this study, a method based on solid phase extraction (SPE) combined with ultra performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-MS/MS) was developed to determine 13 HBQs, including six chlorobenzoquinones, six bromobenzoquinones, and one iodobenzoquinone, in drinking water. One-liter water samples were added with 2.5 mL of formic acid, and 500 mL of each sample was collected for further enrichment. Pretreatment optimization mainly focused on the SPE column, washing solvent, and nitrogen blowing temperature. After extraction using Plexa SPE columns (200 mg/6 mL), the samples were washed with ultrapure water containing 0.25% formic acid combined with 30% methanol aqueous solution containing 0.25% formic acid, eluted with 6 mL of methanol containing 0.25% formic acid, and then nitrogen blown at 30 ℃. The UPLC-MS/MS parameters were optimized by comparing the results of two reversed-phase columns (BEH C18 and HSS T3) and various concentrations of formic acid in the mobile phase, as well as by establishing the best instrumental conditions. The separation of 13 HBQs was performed using an HSS T3 column (100 mm×2.1 mm, 1.8 μm) via gradient elution with a mixture of 0.1% formic acid aqueous solution and methanol as the mobile phase for 16 min. The 13 HBQs were detected using a triple quadrupole mass spectrometer equipped with a negative electrospray ionization source (ESI-) in multiple reaction monitoring (MRM) mode. Matrix-matched calibration curves were used to quantify the HBQs owing to intense matrix inhibitory effects. The results reflected the good linear relationships of the 13 HBQs and yielded correlation coefficients (r) greater than 0.999. The method detection limits (MDLs, S/N=3) were 0.2-10.0 ng/L, while the method quantification limits (MQLs, S/N=10) were 0.6-33.0 ng/L. The recoveries of the 13 HBQs were 56%-88% at three spiked levels (10, 20, 50 ng/L), and the relative standard deviations (RSDs, n=6) were less than or equal to 9.2%. The optimization method was applied to analyze HBQs in five drinking water samples. Four HBQs, namely, 2,6-dichloro-1,4-benzoquinone (2,6-DCBQ), 2,5-dibromo-1,4-benzoquinone (2,5-DBBQ), 2,6-dibromo-1,4-benzoquinone (2,6-DBBQ), and 2,6-dibromo-3,5-dimethyl-1,4-benzoquinone (2,6-DBDMBQ), were detected in the samples with detection rates of 100%, 20%, 80%, and 20%, respectively. The most frequently detected HBQ, 2,6-DCBQ, also exhibited the highest content (15.0-56.2 ng/L). The method showed high sensitivity, stability, accuracy, and efficiency, rendering it suitable for the analysis of 13 HBQs in drinking water. Compared with previous methods that mainly focused on 2,6-DCBQ and 2,6-DBBQ, the developed method achieved higher throughput and enabled the simultaneous analysis of 13 HBQs. The method presented in this study provides an opportunity to explore different types and concentrations of HBQs in drinking water, offers a deeper understanding of the occurrence of HBQs, and facilitates further studies on the health risks and control measures of these compounds.
    Keywords:  disinfection by-products (DBPs); drinking water; halobenzoquinones (HBQs); solid phase extraction (SPE); ultra performance liquid chromatography-triple quadrupole mass spectrometry (UPLC-MS/MS)
  23. Anal Chem. 2023 Jun 02.
      Zebrafish (Danio rerio) represent an effective model biological material for human disease research, even for personalized precision medicine. Thus, it is necessary to fully characterize their molecular information in order to obtain a global metabolic profile. Here, a spatially resolved metabolomics method for whole-body zebrafish analysis was established based on an air-flow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) system. Using the optimized experimental conditions, the method provided high-quality visual distribution information for >1000 functional metabolites, thereby organ-specific metabolites characterizing nine regions were obtained comprehensively, including the eyes, brain, gill, heart, liver, kidney, intestine, muscle, and spinal cord. Then, combined with metabolic pathway analysis, a global metabolic network with in situ information on zebrafish was mapped for the first time. We also tried to use the recently published MSI database to annotate the metabolites in this study; however, the annotation rate was only 33.7 and 10.4% in positive and negative modes, respectively. This further demonstrated the necessity of establishing a suitable AFADESI-MSI method for zebrafish samples. These results offer comprehensive and in-depth molecular information about zebrafish at the metabolic level, which facilitates the use of zebrafish models to understand metabolic reprogramming in human diseases and the development of zebrafish disease models.
  24. J Sep Sci. 2023 Jun 03. e2300210
      Dried blood spot samples are simple to prepare and transport, enabling safe and accessible diagnostics, both locally and globally. We review dried blood spot samples for clinical analysis, focusing on liquid chromatography-mass spectrometry as a versatile measurement tool for these samples. Dried blood spot samples can provide information for, for example, metabolomics, xenobiotic analysis, and proteomics. Targeted analyses of small molecules are the main application of dried blood spot samples and liquid chromatography-mass spectrometry, but emerging applications include untargeted metabolomics and proteomics. Applications are highly varied, including analyses related to newborn screening, diagnostics and monitoring of disease progression and treatment effects of virtually any disease, as well as studies into the physiology and effects of diet, exercise, xenobiotics, and doping. A range of dried blood spot products and methods are available, and applied liquid chromatography-mass spectrometry instrumentation is varied with regard to liquid chromatography column formats and selectivity. In addition, novel approaches such as on-paper sample preparation (e.g., selective trapping of analytes with paper-immobilized antibodies) are described. We focus on research papers published in the last 5 years.
    Keywords:  dried blood spot; liquid chromatography; mass spectrometry; omics; xenobiotics
  25. Ann Nutr Metab. 2023 May 30.
      INTRODUCTION: Vitamin K (VK) as well as vitamin D (VD) play an important role in osteoporosis. Vitamin K1 (VK1) and vitamin K2 (VK2, menaquinone-4 (MK-4) and menaquinone-7 (MK-7)) are significant for the metabolism of skeletal muscle. 25-hydroxyvitamin D2 and 25-hydroxyvitamin D3 (25(OH)D2 and 25(OH)D3) reflect circulating VD levels. More sensitive measurements remains to be developed. In the present study, a new high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the determination of VK1, VK2(MK-4 and MK-7) as well as 25(OH)D2 and 25(OH)D3 levels in human serum.METHODS: We developed a simple LC-MS/MS method for the determination of VK1, MK-4, MK-7, 25(OH)D2 and 25(OH)D3 levels in human serum and validated the method in a study cohort of 200 patients divided into the premenopausal women group and postmenopausal osteoporosis patient group.
    RESULTS: The overall precision (coefficient of variation, CV) ranged from 2.66-10.11% in the specified working range (0.05-5 ng/mL) for VK1, MK-4 and MK-7. Serum VK1, MK-4 and MK-7 levels in postmenopausal women with osteoporosis were 1.187 ± 0.0.094 ng/mL, 0.058 ± 0.009 ng/mL and 0.885 ± 0.064 ng/mL, respectively (mean ± standard deviation, SD). Serum VK1, MK-4 and MK-7 levels in premenopausal women were 1.143 ± 0.103 ng/mL, 0.028 ± 0.003 ng/mL and 1.553 ± 0.226 ng/mL, respectively. Serum 25(OH)D2 and 25(OH)D3 levels in postmenopausal women with osteoporosis were 0.757 ± 0.056 ng/mL and 11.72 ± 0.632 ng/mL, respectively. Serum 25(OH)D2 and 25(OH)D3 levels in premenopausal were 1.793 ± 0.575 ng/mL and 12.42 ± 1.069 ng/mL, respectively.
    CONCLUSION: A new LC-MS/MS method for determination of serum VK and VD levels was evaluated and validated. MK-7 in plasma decreased earlier than VD in postmenopausal osteoporosis patients. MK-7 status is significantly associated with osteoporosis and could be considered a predictable biomarker in the diagnosis of osteoporosis in postmenopausal women.
  26. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2023 May 20. 41(5): 364-366
      Objective: To establish a method for the rapid determination of acetaminophen (APAP) in human plasma by LC-MS/MS. Methods: The plasma samples were extracted by methanol and acetonitrile (1: 1) and purified directly. C(18) column was used for sample separation. The mobile phase were methanol (5 mmol/L ammonium acetate) and water (5 mmol/L ammonium acetate). Samples were analyzed by LC MS/MS with the electrospray ionization multi reaction monitoring (MRM) mode. Results: The calibration curves of APAP was linear in the concentration range of 0~10 mg/L, the correlation coefficient (r) was greater than 0.999 0. The relative standard deviation within and between batches was less than 10%. The recovery rate were 96.81%~101.7%. The detection limit of the method was 0.1 μg/L and the lower limit of quantification was 0.3 μg/L. Conclusion: This method has strong specificity, high sensitivity and reliable determination results. It is suitable for the rapid analysis of clinical plasma samples.
    Keywords:  Acetaminophen; Blood drug concentration; Drug poisoning; LC-MS/MS; Plasma
  27. Magn Reson Chem. 2023 Jun 02.
      We report the development of a software program, called MagMet-F, that automates the processing and quantification of 1D 1 H NMR of human fecal extracts. To optimize the program, we identified 82 potential fecal metabolites using 1D 1 H NMR of six human fecal extracts using manual profiling and a literature review of known fecal metabolites. We acquired pure versions of those metabolites and then acquired their 1D 1 H NMR spectra at 700 MHz to generate a fecal metabolite spectral library for MagMet-F. The fitting of these metabolites by MagMet-F was iteratively optimized to replicate manual profiling. We validated MagMet-F's automated profiling using a test set of six fecal extracts. It correctly identified 80% of the compounds and quantified those within <20% of the values determined by manual profiling using Chenomx. We also compared MagMet-F's profiling performance to two other open-access NMR profiling tools, Bayesil and Batman. MagMet-F outperformed both. Bayesil repeatedly overestimated metabolite concentrations by 10% to 40% while Batman was unable to properly quantify any compounds and took 10-20× longer. We have implemented MagMet-F as a freely accessible web server to enable automated, fast and convenient 1D 1 H NMR spectral profiling of fecal samples. MagMet-F is available at
    Keywords:  1H NMR; automation; fecal extracts; fecal spectral library; metabolite identification; metabolite quantification; software
  28. Sci Total Environ. 2023 May 29. pii: S0048-9697(23)03046-2. [Epub ahead of print] 164425
      Although different quantification methods are extensively used in environmental chemistry, the impact of the choice of method on the quality and range of analytical results is understudied. This two-part study consists of (a) in-lab evaluation and (b) a traditional meta-analysis (n = 66) of commonly used quantification methods): (i) external calibration; (ii) isotope dilution method with authentic target analogs; (iii) isotope dilution with non-target standards; and (iv) standard addition prior to LC-MS/MS in liquid chromatography tandem mass spectrometry (LC-MS/MS) by example of antibiotics in sewage sludge from across the U.S. Using method (i) as the benchmark quantification method for the antibiotic erythromycin in biosolids, other quantification methods resulted in an overestimation (110-450 %) or an underestimation (10-60 %). Using the method (iv) as the benchmark for other compounds resulted in an overestimation (101-14,700 %) or an underestimation (6-98 %). Matrix effects were also observed and were dependent on the matrix and analyte type. For example, in the case of erythromycin, all sample matrices showed signal suppression. This study showed that in the absence of isotopically labeled analogs, the most accurate alternate quantification method may need to be experimentally determined depending on the analyte. Analysis of published literature on pharmaceuticals in sewage sludge indicated that isotope dilution with authentic target analog is most commonly used, followed by non-target isotope standards, standard addition, and finally external calibration.
    Keywords:  Antibiotics; Biosolids; Environmental analytical chemistry; External calibration; Isotopic dilution; Standard addition