bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2022‒01‒30
23 papers selected by
Sofia Costa
Icahn School of Medicine at Mount Sinai

  1. Biomed Chromatogr. 2022 Jan 26.
      Chinese hamster ovary (CHO) cells have been widely used in the biopharmaceutical industry for production of therapeutic proteins. CHO cells in fed-batch cultures produce various amino acid-derived intermediate metabolites. These small molecule metabolic byproducts have proven to be critical to cell growth, culture performance, and more interestingly antibody drug productivity. Herein, we developed a liquid chromatography - high resolution mass spectrometry (LC-HRMS) based targeted metabolomics approach for comprehensive quantification of total 21 growth inhibition related metabolites generated from 14 different amino acids in CHO cell fed-batch cultures. High throughput derivatization procedures, matrix-matched calibration curves, stable isotope-labeled internal standards, and accurate mass Full MS scan were utilized in order to achieve our goal for wide scope of metabolite screening as well as validity and reliability of metabolite quantification. We further present a novel analytical strategy for extending the assay's dynamic range by utilizing naturally occurring isotope M+1 ion as a quantification analogue in the circumstances where the principal M ion is beyond its calibration range. The integrated method was qualified for selectivity, sensitivity, linearity, accuracy, precision, isotope analysis and other analytical aspects to demonstrate assay robustness. We then applied this metabolomics approach to characterize metabolites of interest in a CHO cell based monoclonal antibody (mAb) production process with fed-batch bioreactor culture mode. Absolute quantification combined with multivariate statistical analysis illustrated that our target analytes derived from amino acids, especially from branched-chain amino acids, closely correlated with cell viability and significantly differentiated cellular stages in production process.
    Keywords:  Bioprocessing; CHO Cell Culture; LC-HRMS; Quantitative; Targeted Metabolomics
  2. J Chromatogr A. 2022 Jan 15. pii: S0021-9673(22)00030-9. [Epub ahead of print]1665 462832
      The applicability of ultrahigh-performance supercritical fluid chromatography coupled with mass spectrometry (UHPSFC/MS) for the qualitative analysis of metabolites with a wide polarity range (log P: -3.89-18.95) was evaluated using a representative set of 78 standards belonging to nucleosides, biogenic amines, carbohydrates, amino acids, and lipids. The effects of the gradient shape and the percentage of water (1, 2, and 5%) were investigated on the Viridis BEH column. The screening of eight stationary phases was performed for columns with different interaction sites, such as hydrogen bonding, hydrophobic, π-π, or anionic exchange type interactions. The highest number of compounds (67) of the set studied was detected on the Torus Diol column, which provided a resolution parameter of 39. The DEA column had the second best performance with 58 detected standards and the resolution parameter of 54. The overall performance of other parameters, such as selectivity, peak height, peak area, retention time stability, asymmetry factor, and mass accuracy, led to the selection of the Diol column for the final method. The comparison of additives showed that ammonium acetate gave a superior sensitivity over ammonium formate. Moreover, the influence of the ion source on the ionization efficiency was studied by employing atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI). The results proved the complementarity of both ionization techniques, but also the superior ionization capacity of the ESI source in the negative ion mode, for which 53% of the analytes were detected compared to only 7% for the APCI source. Finally, optimized analytical conditions were applied to the analysis of a pooled human plasma sample. 44 compounds from the preselected set were detected in human plasma using ESI-UHPSFC/MS in MSE mode considering both ionization modes.
    Keywords:  Amino acids; Human plasma; Mass spectrometry; Metabolites; Supercritical fluid chromatography
  3. Bioinformatics. 2022 Jan 26. pii: btac040. [Epub ahead of print]
      MOTIVATION: Robust and reproducible data is essential to ensure high-quality analytical results and is particularly important for large-scale metabolomics studies where detector sensitivity drifts, retention time and mass accuracy shifts frequently occur. Therefore, raw data needs to be inspected before data processing in order to detect measurement bias and verify system consistency.RESULTS: Here we present RawHummus, an R Shiny app for an automated raw data quality control in metabolomics studies. It produces a comprehensive quality control report, which contains interactive plots and tables, summary statistics and detailed explanations. The versatility and limitations of RawHummus are tested with thirteen metabolomics/lipidomics datasets and one proteomics dataset obtained from five different liquid chromatography mass spectrometry platforms.
    AVAILABILITY: RawHummus is released on CRAN repository (, with source code being available on GitHub ( The web application can be executed locally from the R console using the command "runGui()". Alternatively, it can be freely accessed at
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
  4. Anal Chem. 2022 Jan 25.
      Sodium and potassium are biological alkali metal ions that are essential for the physiological processes of cells and organisms. In combination with small-molecule metabolite information, disturbances in sodium and potassium tissue distributions can provide a further understanding of the biological processes in diseases. However, methods using mass spectrometry are generally tailored toward either elemental or molecular detection, which limits simultaneous quantitative mass spectrometry imaging of alkali metal ions and molecular ions. Here, we provide a new method by including crown ether molecules in the solvent for nanospray desorption electrospray ionization mass spectrometry imaging (nano-DESI MSI) that combines host-guest chemistry targeting sodium and potassium ions and quantitative imaging of endogenous lipids and metabolites. After evaluation and optimization, the method was applied to an ischemic stroke model, which has highly dynamic tissue sodium and potassium concentrations, and we report 2 times relative increase in the detected sodium concentration in the ischemic region compared to healthy tissue. Further, in the same experiment, we showed the accumulation and depletion of lipids, neurotransmitters, and amino acids using relative quantitation with internal standards spiked in the nano-DESI solvent. Overall, we demonstrate a new method that with a simple modification in liquid extraction MSI techniques using host-guest chemistry provides the added dimension of alkali metal ion imaging to provide unique insights into biological processes.
  5. Biomed Chromatogr. 2022 Jan 24. e5347
      In recent years, LC-MS/MS has become a fundamental technology in clinical practice. In Japan, the LC-MS/MS system is used in many large hospitals, and it has become popular among pharmacists and laboratory technicians. LC-MS/MS has some advantages in terms of accuracy, speed, and comprehensiveness compared to conventional automated chemical testing equipment. However, LC-MS/MS is by no means a universal method, and it is necessary to understand its characteristics before using it. In the TDM region, there is an issue with linearity in comprehensive measurement; however, an ion abundance adjustment method such as in-source collision-induced dissociation has been proposed as a solution to this problem. The development of a biomarker analysis includes searching, identification, and quantification, and it is necessary to select an appropriate mass spectrometric method for each step. In this paper, we review cutting-edge technologies that can expand the performance of LC-MS/MS in the clinical field as well as consider current issues and future prospects.
    Keywords:  LC-MS/MS; biomarkers; clinical research; hospital pharmacists; mass spectrometry; therapeutic drug monitoring
  6. Anal Bioanal Chem. 2022 Jan 26.
      Mass spectral library annotation of liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) data is a reliable approach for fast identification of organic contaminants and toxicants in complex environmental and biological matrices. While determining the exposure of humans or mammals, it is indispensable to include phase I and phase II metabolites (conjugates) along with the parent compounds, but often, tandem mass spectra for these are unavailable. In this study, we present and evaluate a strategy for annotating glucuronide conjugates in LC-HRMS/MS scans by applying a neutral loss search for detection, then truncating the spectra which we refer to as in silico deconjugation, and finally searching these against mass spectral libraries of the aglycones. The workflow was tested on a dataset of in vitro-generated glucuronides of reference standard mixtures and a dataset of 51 authentic urine samples collected from patients with known medication status, acquired on different instrumentations. A total number of 75 different glucuronidated molecular structures were identified by in silico deconjugation and spectral library annotation. We also identified specific molecular structures (sulfonamides, ether bonds, di-glucuronides), which resulted in slightly different fragmentation patterns between the glucuronide and the unconjugated compound. This led to a decreased spectral matching score and in some cases to a false-negative identification. Still, by applying this method, we revealed a reliable annotation of most common glucuronides, leading to a new strategy reducing the need for deconjugation steps or for recording many reference glucuronide spectra for screening approaches.
    Keywords:  Drug monitoring/drug screening; Glucuronide; Human biomonitoring; Mass spectrometry; Metabolites; Spectral library search
  7. J Am Soc Mass Spectrom. 2022 Jan 25.
      LC-MS is a key technique for the identification of small molecules in complex samples. Accurate mass, retention time, and fragmentation spectra from LC-MS experiments are compared to reference values for pure chemical standards. However, this information is often unavailable or insufficient, leading to an assignment to a list of candidates instead of a single hit; therefore, additional features are desired to filter candidates. One such promising feature is the number of specific functional groups of a molecule that can be counted via derivatization or isotope-exchange techniques. Hydrogen/deuterium exchange (HDX) is the most widespread implementation of isotope exchange for mass spectrometry, while oxygen 16O/18O exchange is not applied as frequently as HDX. Nevertheless, it is known that some functional groups may be selectively exchanged in 18O enriched media. Here, we propose an implementation of 16O/18O isotope exchange to highlight various functional groups. We evaluated the possibility of using the number of exchanged oxygen atoms as a descriptor to filter database candidates in untargeted LC-MS-based workflows. It was shown that 16O/18O exchange provides 62% (median, n = 45) search space reduction for a panel of drug molecules. Additionally, it was demonstrated that studying the fragmentation spectra after 16O/18O can aid in eliminating false positives and, in some cases, help to annotate fragments formed with water traces in the collisional cell.
    Keywords:  LC−MS; drugs; identification; isotope exchange; mass spectrometry; metabolomics; stable isotopes
  8. Se Pu. 2022 Feb 08. 40(2): 123-129
      Osteonecrosis of the femoral head (ONFH) can lead to its collapse which requires total hip arthroplasty. Exosomes, which are important for intercellular communication are involved in a series of physiological and pathological processes, and therefore play a unique role in disease diagnosis and treatment. In this study, untargeted metabolomics was used to investigate the metabolic characteristics of lipids in exosomes of femoral head tissue with osteonecrosis and to explain the metabolic changes that occur in the body during this disease. Ultracentrifugation was used to separate and enrich exosomes from femoral head tissue with osteonecrosis. Exosomes were identified using dynamic light scattering (DLS), Western blotting, and transmission electron microscopy (TEM). Gradient elution was performed with ultrapure water and acetonitrile as mobile phases using a Kinetex XB-C18 column (100 mm×2.1 mm, 2.6 μm). The column oven temperature, flow rate of the mobile phase, and duration were 30 ℃, 300 μL/min, and 15 min, respectively. A triple TOF 4600 high resolution mass spectrometry system was used, and the mass scan range of m/z was set at 100 -1000. Other conditions were as follows: sheath gas, 380 kPa; auxiliary gas, 380 kPa; curtain gas, 170 kPa; and atomization temperature, 600 ℃. Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) combined with multivariate statistical analysis was used to identify the lipid metabolic profile of ONFH-derived exosomes. The exosome metabolites were characterized in detail, which enables their identification and provided a reliable method for quality evaluation. After transforming the obtained original data using MarkView software, peak identification, peak alignment, subtraction of solvent peak, impurity peak, noise filtering, and other treatments, a three-dimensional matrix was obtained from the exported data table. Principal component analysis (PCA) and orthogonal partial least squares discrimination analysis (OPLS-DA) in the SIMCA-P14.1 software were used for multivariate statistical analysis of differentially expressed exosome lipid metabolites. This strategy was validated using lipid metabolites from patients with ONFH and healthy controls. The correlation distribution was shown according to the point dispersion of the PCA score plot, and lipid metabolites from the same disease showed ideal clustering. This result indicates a small difference between the groups. A good clustering effect is also obtained using OPLS-DA, and the statistical model has high reliability. A total of 18 significantly altered lipid metabolites were detected in the exosomes, including acrylolipids, fatty acid esters, glycerides, and their derivatives. The pathway analysis was conducted with MetaboAnalyst ( via database source including the HMDB ( and MMCD ( for confirming the impacted metabolic pathways and visualization. Metabolic pathway analysis showed that glycerophospholipid and sphingolipid metabolism were the most significantly altered in exosomes. An imbalance between sphingolipids and glycerophospholipids leads to lipotoxic damage, which is implicated in the pathophysiology of common metabolic diseases. Furthermore, glycerophospholipids are correlated with cell proliferation, differentiation, and apoptosis, and the change in glycerophospholipid ratio can reflect the disturbance in lipid metabolism. The metabolic changes in exosomes may reflect the metabolic changes in ONFH. In this study, lipid metabolomics analysis based on UPLC-MS/MS was used to determine metabolic differences between exosomes extracted from ONFN and femoral neck fracture (FNF). Metabolomic analysis of necrotic femoral head tissue-derived exosomes can help explore the most relevant pathways for assessing the changes in exosome metabolism that affect exosome metabolism in necrotic bone tissue.
    Keywords:  exosomes; lipid; metabolic pathway; metabolomics; osteonecrosis of the femoral head (ONFH); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  9. J Mass Spectrom Adv Clin Lab. 2022 Jan;23 58-70
      Mass spectrometry imaging (MSI) has emerged as a rapidly expanding field in the MS community. The analysis of large spectral data is further complicated by the added spatial dimension of MSI. A plethora of resources exist for expert users to begin parsing MSI data in R, but there is a critical lack of guidance for absolute beginners. This tutorial is designed to serve as a one-stop guide to start using R with MSI data and describe the possibilities that data science can bring to MSI analysis.
    Keywords:  AuNP, gold nanoparticle; Cardinal; DESI, desorption electrospray ioniziation; Data validation; IACUC, Institutional Animal Care and Use Committee; ITO, indium tin oxide; MSI, mass spectrometry imaging; Mass spectrometry imaging; PCA, principal component analysis; R Studio; RAM, random access memory; RMS, root mean squared; SNR, signal to noise ratio; SSC, spatial shrunken centroid; SSD, solid state drive; TIC, total ion current
  10. Anal Chem. 2022 Jan 27.
      Bile acids (BAs) are a type of gut microbiota-host cometabolites with abundant structural diversity, and they play critical roles in maintaining host-microbiota homeostasis. In this study, we developed a new N-(4-aminomethylphenyl) pyridinium (AMPP) derivatization-assisted alternating dual-collision energy scanning mass spectrometry (AMPP-dual-CE MS) method for the profiling of BAs derived from host-gut microbiota cometabolism in mice. Using the proposed method, we discovered two new types of amino acid conjugations (alanine conjugation and proline conjugation) and acetyl conjugation with host BAs, for the first time, from mouse intestine contents and feces. Additionally, we also determined and identified nine new leucine- and phenylalanine-conjugated BAs. These findings broaden our knowledge of the composition of the BA pool and provide insight into the mechanism of host-gut microbiota cometabolism of BAs.
  11. Anal Bioanal Chem. 2022 Jan 23.
      Sphingolipids are a class of lipids with high structural diversity and biological pleiotropy. Mounting evidence supports a role for sphingolipids in regulating pathophysiology of cardiometabolic diseases, and they have been proposed as potential cardiometabolic biomarkers. Current methods for quantifying sphingolipids require laborious pretreatment and relatively large sample volumes, and cover limited species, hindering their application in epidemiological studies. Herein, we applied a time-, labor-, and sample-saving protocol simply using methanol for plasma sphingolipid extraction. It was compared with classical liquid-liquid extraction methods and showed significant advantages in terms of simplicity, sphingolipid coverage, and sample volume. By coupling the protocol with liquid chromatography using a wide-span mobile phase polarity parameter and tandem mass spectrometry operated in dynamic multiple reaction monitoring mode, 37 sphingolipids from 8 classes (sphingoid base, sphingoid base phosphate, ceramide-1-phosphate, lactosylceramide, hexosylceramide, sphingomyelin, ceramide, and dihydroceramide) were quantified within 16 min, using only 10 μL of human plasma. The current method showed good performance in terms of linearity (R2 > 0.99), intra- and interbatch accuracy (70-123%) and precision (RSD < 12%), matrix effect (91-121%), recovery (96-101%), analyte chemical stability (deviation < 19%), and carryover (< 16%). We successfully applied this method to quantify 33 detectable sphingolipids from 579 plasma samples of an epidemiological study within 10 days. The quantified sphingolipid concentrations were comparable with previous studies. Positive associations of ceramide C22:0/C24:0 and their precursors with homeostasis model assessment of insulin resistance suggested that the synthesis of the ceramides might be involved in insulin resistance. This novel method constitutes a simple and rapid approach to quantify circulating sphingolipids for epidemiological studies using targeted lipidomic analysis, which will help elucidate the sphingolipid-regulated pathways underlying cardiometabolic diseases.
    Keywords:  Cardiometabolic diseases; LC–MS/MS; Lipidomics; Plasma; Sphingolipids
  12. Se Pu. 2022 Feb 08. 40(2): 165-174
      Corticosteroids (CSs) are widely used to treat various inflammatory and immune diseases in humans and animals, such as arthritis and lupus. Thus far, CSs have been frequently detected in diverse pollution sources, such as in the influent and effluent of traditional wastewater treatment plants, livestock farms, and aquaculture. Owing to incomplete removal or limited treatment, CSs can enter the water environment and eventually be adsorbed in the sediment. Due to hydrodynamic effects, CSs can re-enter the surface water through the resuspension of sediments, and pose a hazard to the ecosystem and human health via the enrichment of aquatic organisms and transmission through the food chain. Therefore, trace analysis of CSs in sediments is significant for exploring their prevalence and behavior in multiple environments. However, existing research mainly focuses on the determination of glucocorticoids in water samples, and studies on the systematic quantitative analysis of CSs in environmental solid samples with more complex matrices are scarce. Moreover, majority of previous investigations focused on a limited number of glucocorticoids, making it important to widen the range of target compounds to be studied, including mineralocorticoids. In this study, the main factors which could influence the accuracy and sensitivity in the determination of 24 target CSs were systematically optimized in the sample pretreatment and instrument analysis. A novel method based on ultrasonic extraction coupled with solid phase extraction (SPE) for sample pretreatment was developed for the simultaneous determination of the 24 CSs in sediments using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The sediment sample was ground to homogenize the particle sizes after freeze-drying. The analytes from 2.0 g of the sample were ultrasonicated and extracted with methanol-acetone (1∶1, v/v). After concentrating and diluting each extract, SPE was performed. The water sample was extracted and purified using hydrophile-lipophile balance (HLB) cartridges, following which the extract was further purified with LC-NH2 cartridges. The extracts were concentrated using a rotary evaporator, dried under a gentle stream of nitrogen, and re-dissolved in methanol for instrumental analysis. Chromatographic separation was conducted on an Agilent ZORBAX Eclipse Plus C8 column (100 mm×2.1 mm, 1.8 μm), with a column flow rate of 0.3 mL/min and a gradient of mobile phases A (water with 0.1% acetic acid) and B (acetonitrile). The column temperature was set to 30 ℃ and the injection volume was fixed at 5 μL. Electrospray ionization MS in the dynamic multiple reaction monitoring (DMRM) and selected ion monitoring (SIM) modes were performed in the positive mode for the qualitative and quantitative analysis of the target compounds. Quantitation of the target compounds was carried out using the internal standard method. The effects of different extraction solvents, purification conditions, and MS conditions on the recoveries of the target compounds were investigated. The limits of detection (LODs) (S/N≥3) and limits of quantification (LOQs) (S/N≥10) of all 24 compounds were in the ranges of 0.14-1.25 μg/kg and 0.26-2.26 μg/kg, respectively. The correlation coefficients of linear calibration curves were higher than 0.995 in the range of 1.0-100 μg/L. The recoveries of the 24 CSs at 5, 20, and 50 μg/kg spiked levels ranged from 64.9% to 125.1% with relative standard deviations of 0.4%-12.6% (n=5). The developed method was applied to analyze the CSs in three sediment samples from the rivers of the Pearl River Delta. In all, 11 target compounds were detected in these samples, with contents in the range of 1.25-29.38 μg/kg. The characteristic of this method is efficient, sensitive, reliable, and suitable for the trace determination of varieties of natural and synthesized CSs in environmental sediments.
    Keywords:  corticosteroids; sediments; solid phase extraction (SPE); ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS); ultrasonic extraction
  13. Se Pu. 2022 Feb 08. 40(2): 206-211
      The residues of fipronil and its metabolites, namely fipronil-desulfinyl, fipronil-sulfone, and fipronil-sulfide, have attracted increasing attention since the European egg contamination incident. In this study, by optimizing the pretreatment method and chromatographic conditions, a simple extraction method coupled with high performance liquid chromatography-tandem mass spectrometry was developed for the simultaneous determination of fipronil and its metabolites, including fipronil-desulfinyl, fipronil-sulfone, and fipronil-sulfide, in livestock and poultry liver. The optimal pretreatment method for fipronil and its metabolites was determined by comparing the recoveries obtained with different extraction solvents (methanol, acetonitrile, acetone, and ethyl acetate), and by purification with N-propyl ethylenediamine (PSA) and octadecylsilane (C18). The samples were extracted with 10 mL acetonitrile, then purified with 150 mg PSA and 100 mg C18, following which the extracted solutions were directly injected for analysis. Separation was performed on an Agilent ZORBAX SB-C18 column (150 mm×2.1 mm, 3.5 μm) with gradient elution using acetonitrile and water as the mobile phases. The target compounds were detected by electrospray ionization (ESI) in the negative mode under multiple reaction monitoring, and quantified by the external standard method with matrix-matched standard correction curves. The results indicated that the linear ranges for the four compounds ranged from 0.1 μg/L to 10.0 μg/L with correlation coefficients (r2) higher than 0.995. The limit of detection was 0.2 μg/kg and limit of quantitation was 0.5 μg/kg. The average recoveries were between 81.1% and 99.8% at three spiked levels of 0.5, 1.0, and 10 μg/kg, with relative standard deviations (RSDs) of 6.1%-11.7%. The matrix effect experiment showed that fipronil and its metabolites had matrix inhibition effects. Matrix-matched standard curve correction was performed to eliminate matrix inhibition effects. The proposed method was used for the analysis of 99 liver samples, where fipronil-sulfone was detected in four samples with values of 1.25-2.82 μg/kg. The method is simple, sensitive, and accurate, and is suitable for the determination of fipronil and its metabolites in livestock and poultry liver.
    Keywords:  dispersive solid phase extraction (dSPE); fipronil and its metabolites; high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS); livestock and poultry liver
  14. Pharmacology. 2022 Jan 27. 1-8
      INTRODUCTION: A simple, sensitive, rapid, and practical 2-dimensional liquid chromatography (2D-LC) method was developed and validated for the quantification of a 500-μL afatinib sample extracted from human plasma.METHODS: The plasma samples were pretreated with acetonitrile for protein precipitation. The mobile phase consisted of a first-dimensional mobile phase (acetonitrile, methanol, and 25 mmol/L ammonium phosphate in a ratio of 25:25:50, V/V/V) and a second-dimensional mobile phase (acetonitrile and 10 mmol/L ammonium phosphate in a ratio of 25:75, V/V). The average recovery of the plasma samples was stable and reproducible (98.56%-100.02%).
    RESULTS: The analyte was sufficiently stable for handling and analysis. The calibration curve was linear, ranging from 10.93 to 277.25 ng/mL with regression equation y = 804.60 x - 4,169.87 (R2 = 0.999). The relative standard deviations for accuracy and precision studies were within ±2.30% and <3.41%, respectively (intra- and interday). Finally, the validated method was successfully employed to determine the drug levels in plasma from the patients treated with afatinib. In clinical assessment, the patients with gastric cancer were orally administered with 30 or 40 mg per day of afatinib, which resulted in large plasma concentrations, ranging from 5.52 to 45.16 ng/mL.
    CONCLUSION: The results indicated that this method was useful for the therapeutic drug monitoring of afatinib and suitable for the assessment of the risks and benefits of chemotherapy in patients with non-small cell lung cancer.
    Keywords:  2-Dimensional liquid chromatography; Afatinib; Cancer patients; Therapeutic drug monitoring
  15. J Am Soc Mass Spectrom. 2022 Jan 24.
      Infrared matrix-assisted laser desorption ionization (IR-MALDESI) is a hybrid mass spectrometry ionization source that combines the benefits of electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) making it a great analytical tool for high-throughput screening (HTS) analyses. IR-MALDESI is coupled to an Orbitrap Exploris 240 mass spectrometer that utilizes a bent quadrupole (C-trap) to inject accumulated ions into the high-field Orbitrap mass analyzer. Here, we present a study on the optimized C-trap timing for HTS analyses by IR-MALDESI mass spectrometry. The timing between initial ion generation and the C-trap opening time was optimized to reduce unnecessary ambient ion accumulation in the mass spectrometer. The time in which the C-trap was held open, the ion accumulation time, was further optimized to maximize the accumulation of analyte ions generated using IR-MALDESI. The resulting C-trap opening scheme benefits small-molecule HTS analyses by IR-MALDESI by maximizing target ion abundances, minimizing ambient ion abundances, and minimizing the total analysis time per sample. The proposed C-trap timing scheme for HTS does not translate to large molecules; a NIST monoclonal antibody standard reference material was analyzed to demonstrate that larger analytes require longer ion accumulation times and that IR-MALDESI can measure intact antibodies in their native state.
    Keywords:  C-trap; IR-MALDESI; Orbitrap mass spectrometer; high-throughput screening
  16. Se Pu. 2022 Feb 08. 40(2): 130-138
      Disulfoton, an organophosphorus pesticide, is used to control cotton, beet, potato, and other seedling period aphids, leaf moths, underground pests, etc., with internal absorption, killing, gastric poisoning, and fumigation. Disulfoton is a highly toxic organophosphate pesticide, which can inhibit cholinesterase activity, resulting in neurophysiological disorders by inhalation, feeding, and transdermal absorption. Disulfoton is difficult to degrade in the environment, which leads to enrichment in organisms and interference with endocrine. This compound is harmful to the ecological environment and human health. To ensure the quality and safety of food, it is important to develop a detection method for disulfoton and its metabolites in agricultural products. A reliable method based on dispersive solid phase extraction (d-SPE) with ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was developed for the determination of disulfoton and its metabolites (disulfoton sulfone, disulfoton sulfoxide, demeton-S, demeton-S sulfone, and demeton-S sulfoxide) in agricultural products (pea, asparagus, wheat, coffee bean, and peanut). The optimal extraction method was as follows: 5.0 g the samples were extracted with acetonitrile (wheat, coffee bean, and peanut presoaked in 5 mL water) in a 50 mL centrifuge tube, followed by 10 min vortex. Before 30 s vortex, 4 g NaCl was added. After 5 min centrifugation, 1.5 mL of the supernatant was cleaned up with 50 mg octadecylsilane bonded silica (C18), 50 mg primary secondary amine (PSA), and 50 mg aminopropyl (NH2) adsorbents. The analytes were separated on a Thermo Syncronis C18 column (150 mm×2.1 mm, 5 μm) with gradient elution using water and acetonitrile at a column temperature of 40 ℃. The injection volume was 2 μL. Disulfoton and its metabolites were analyzed in multiple reaction monitoring (MRM) mode with positive electrospray ionization (ESI+) for the selective quantification. Qualitative and quantitative analyses were accorded to the retention times and characteristic ion pairs with one parent ion and two fragment ions. Quantitative analysis was performed by an external standard method using matrix-matched calibration curves. All the parameters that affected the extraction efficiencies were optimized. C18, PSA, and NH2 gave good recoveries of 87.9%-109.0%. Other adsorbents, multiwalled carbon nanotubes (MWCNTs), hydroxylated multiwalled carbon nanotubes (OH-MWCNTs), carboxylated multiwalled carbon nanotubes (COOH-MWCNTs), octylsilane bonded silica (C8), strong cation exchange (SCX) and neutral alumina (N-Al2O3), led to recoveries below 56.2%. The combination of adsorbents was also considered. Seven different combinations of 50 mg C18, 50 mg PSA, and 50 mg NH2 were chosen for the optimization experiments. There were no obvious differences in these combinations, and the target analytes recoveries ranged from 81.0% to 109.3% with relative standard deviations (RSDs) between 0.6% and 12.5%. The matrix effect could affect the extraction efficiency. The adsorbents of 50 mg C18, 50 mg PSA, and 50 mg NH2 showed weaker matrix effects as compared with other combinations of adsorbents in the instrument. The results for the matrix effect showed that peanuts and asparagus exceeded 20%, requiring matrix-matched calibration curves. Under the optimized conditions, disulfoton and its metabolites showed good linearities (R2≥0.9981) in the range of 2.0-200.0 μg/L. The average spiked recoveries of disulfoton and its metabolites in peas, asparagus, wheat, peanuts, and coffee beans ranged from 75.0% to 110.0%, with RSDs of 0.7% to 14.9%. The limits of detection (LODs) were between 0.02 and 2.0 μg/kg, and the limits of quantification (LOQs) were 5.0 μg/kg. The method was applied for the detection of 80 commercial productions, and neither disulfoton nor its metabolites were found. The proposed method is rapid, accurate, highly selective, and sensitive, and it is suitable for the simultaneous determination of disulfoton and its metabolites in grain, oil crops, vegetables, and other matrices.
    Keywords:  agricultural products; dispersive solid phase extraction (d-SPE); disulfoton; metabolites; ultra high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS)
  17. Sci Rep. 2022 Jan 27. 12(1): 1478
      We provide a pipeline for data preprocessing, biomarker selection, and classification of liquid chromatography-mass spectrometry (LCMS) serum samples to generate a prospective diagnostic test for Lyme disease. We utilize tools of machine learning (ML), e.g., sparse support vector machines (SSVM), iterative feature removal (IFR), and k-fold feature ranking to select several biomarkers and build a discriminant model for Lyme disease. We report a 98.13% test balanced success rate (BSR) of our model based on a sequestered test set of LCMS serum samples. The methodology employed is general and can be readily adapted to other LCMS, or metabolomics, data sets.
  18. Se Pu. 2022 Feb 08. 40(2): 148-155
      β-Agonists, β-blockers, and protein assimilators are classified as stimulant drugs. Their illegal use during animal feeding and slaughtering leads to food-borne stimulant drug residues, which are harmful to human health. At present, methods for the detection of β-agonists and protein assimilators are prevalent, but those for the detection of β-blockers are rare. There is no national standard for the detection of β-blockers in food products of animal origin. A method based on ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed for the determination of nine food-borne stimulant drug residues, including β-agonists, β-blockers, and protein assimilators, in pork, egg, and milk. The optimal extraction conditions for this method were as follows: The samples were hydrolyzed with β-glucuronidase/aryl sulfate esterase in pH 5.2 ammonium acetate buffer. Enzymatic hydrolysis was carried out in a constant-temperature (37 ℃) water bath oscillator for 16 h. The enzymolyzed samples were cooled to room temperature and then extracted with acetonitrile, which was adjusted to pH 9.5 with NaOH solution. After extraction and homogeneous mixing, the extract was added to a salt package for salting out stratification. The clear supernatant was cleaned up using an enhanced lipid removal tube (EMR-lipid), which was pre-activated by water. Then, anhydrous magnesium sulfate was added to ensure dehydration of the extract and concentrated to near dryness under nitrogen flow. The residue was dissolved in 1 mL acetonitrile-0.1% formic acid aqueous solution (1∶9, v/v). Separation was performed on an ACQUITY UPLC HSS T3 column (100 mm×2.1 mm, 1.8 μm) with gradient elution using methanol-0.1% formic acid aqueous solution as the mobile phase. The analytes were detected in the multiple reaction monitoring (MRM) mode after being ionized by an electrospray positive ion (ESI+). Quantitative analysis was performed by the internal standard method using matrix-matched calibration curves. The effects of the extraction solvent and pH on the extraction efficiency during pretreatment were optimized. The influence factors of different types of chromatographic column, mobile phase and dissolved solution in the process of instrumental analysis were discussed in detail. Under the optimal conditions, the method showed good linearity in the range of 0.5 to 20 μg/L, with correlation coefficients (r2) greater than 0.99. The limits of detection (LODs) and limits of quantification (LOQs) were in the range of 0.3-0.6 μg/kg and 1.0-2.0 μg/kg, respectively. The average recoveries of all the compounds ranged from 65.2% to 117.0% with relative standard deviations (RSDs) in range of 1.3%-14.4% at spiked levels of 1, 2, and 5 times the LOQs. The established method was used to determine the quality of animal-origin foods such as pork, eggs, and milk purchased from the market. The nine stimulant drug residues were not detected in these food samples. The analytical method is rapid, sensitive, accurate, and stable. It can be used for the determination of the nine food-borne stimulant drugs residue in pork, egg, and milk.
    Keywords:  egg; food-borne stimulant drug; milk; pork; residues; ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)
  19. Food Microbiol. 2022 May;pii: S0740-0020(21)00230-6. [Epub ahead of print]103 103964
      Yeast metabolism depends on growing conditions, which include the chemical composition of the medium, temperature and growth time. Historically, fatty acid profiles have been used to differentiate yeasts growing in liquid media. The present study determined the fatty acids of Saccharomyces species in colonies. Using the same method, the effect of that the number of colonies and growth time had on solid media allowed us to determine the metabolomic profiles of the cells. Our results showed that the lipid and metabolomic profiles of the cells evolved as the colony grew. Interestingly, some strains of Saccharomyces cerevisiae have been were differentiated using the fatty acid profile of a colony; concretely indeed EC1118 and QA23 strains were separated from ICV-K1 and BM4x4. The synthesis of saturated fatty acids was greater than that of unsaturated fatty acids during the first two days of cell growth on a solid medium compared to a liquid medium. Unsaturated fatty acids subsequently became predominant. Finally, this methodology could be useful for carrying out physiological studies in a complete or defined solid growth medium allowing the supplementation of compounds, which inhibit or activate the growth of yeasts.
    Keywords:  Fatty acids; S. kudriavzevii; S. uvarum; Saccharomyces cerevisiae; Squalene; Trehalose; Wine yeast
  20. Int J Occup Med Environ Health. 2022 Jan 20. pii: 142527. [Epub ahead of print]
      Lipidomics belongs to the family of the so-called omics domains, which, based on modern chemical technologies, strive to explain the biological principles of the organism's functioning. Main biological functions of lipids include energy storage, the formation of cell membranes, and participation in the transmission of biological signals, and their dysregulation is responsible for the development of pathological states. Thanks to lipid profiling, potential biomarkers for disease diagnosis and prognosis can be identified. This paper discusses selected examples of the use of lipidomic tests in the diagnosis of the kidney, metabolic and neoplastic diseases based on research papers published over the last few years (since 2016). Only works based on the study of human biological material by mass spectrometry methods were taken into account. The examples of lipidomics application presented in this publication are only a few of the possibilities of this technique. As potential possibilities have already been discovered, the next step for the research community is to work on standardization of the approach to lipidomic research and to develop bioinformatics methods that allow efficient processing and analysis of large amounts of data generated in this technique.
    Keywords:  biomarkers; cancer; kidney disease; lipidomics; lipids; metabolomic disease
  21. J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Jan 15. pii: S1570-0232(22)00033-2. [Epub ahead of print]1191 123129
      Contezolid is a novel oxazolidinone antibiotic with good antibacterial activity against gram-positive bacteria including methicillin-resistant Staphylococcus aureus. For the purpose to further characterize the pharmacokinetics of contezolid and its major metabolite M2, accurate and rapid ultra-performance liquid chromatography-tandem mass spectrometric assays (UPLC-MS/MS) were developed and validated for simultaneous quantification of contezolid and M2 in human plasma and urine. The plasma samples were pretreated by liquid-liquid extraction. The automated solid phase extraction method was used to preprocess urine samples. ACQUITY UPLC® BEH C8 (2.1 mm × 100 mm, 1.7 µm) column was used to separate the analytes with a gradient mobile phase of acetonitrile and water at a flow rate of 0.4 mL/min. The calibration curves showed good linearity over the concentration ranges of 0.0100-5.00 µg/mL for contezolid in plasma and urine, 0.00200-1.00 µg/mL in plasma and 0.0200-10.0 µg/mL in urine for M2, respectively. For both plasma and urine assays, the intra- and inter-batch accuracy and precision were within 15% for all quality control levels, including the lower limit of quantitation. The methods were fully validated and successfully applied to a pharmacokinetic study of contezolid tablets in subjects with moderate hepatic impairment.
    Keywords:  Contezolid; Human plasma and urine; Liver impairment; Metabolite; UPLC-MS/MS
  22. Anal Bioanal Chem. 2022 Jan 27.
      Microbial secondary metabolites represent a rich source for drug discovery, plant protective agents, and biotechnologically relevant compounds. Among them are siderophores, iron-chelating molecules, that show a great influence on bacterial community assembly and the potential to control pathogen invasions. One of such a siderophore is pyoverdine that is produced by fluorescent Pseudomonas members and consists of different peptide chains specific to each bacterial species. The identification and structural elucidation of such suites of siderophores remain widely underexplored as general high-throughput analytical protocols are missing. Therefore, a dedicated method was established allowing a rapid localization and structural elucidation of pyoverdines. Liquid bacterial culture samples were purified by an easy small-scale solid-phase extraction (SPE). Ultra-high-performance liquid chromatography high-resolution tandem mass spectrometry (UHPLC-HR-MS/MS) separated highly polar pyoverdines and their derivatives. All ion fragmentation (AIF) generated mass spectra containing the characteristic fragments of the biological precursor of pyoverdine, ferribactin. This led to the revelation of the mass of secreted pyoverdines. Targeted MS/MS experiments at multiple collision energies accomplished the full structure elucidation of the pyoverdine peptide chain. A mass calculator and a fragmentation predictor facilitated greatly the interpretation of MS/MS spectra by providing accurate masses for a straightforward comparison of measured and theoretical values. The method was successfully validated using four well-known pyoverdines with various peptide chains. Finally, the applicability was proven by the analysis of 13 unknown pyoverdines secreted by sampled bacterial cultures. Among these, 4 novel pyoverdine peptide chains were discovered and are herein reported for the first time.
    Keywords:  Ferribactin; High-throughput structure elucidation pipeline; Isopyoverdine; Pseudomonas; Pyoverdine; Siderophore; UHPLC-MS
  23. J Chromatogr A. 2022 Jan 13. pii: S0021-9673(22)00024-3. [Epub ahead of print]1665 462826
      The present work aimed at the development of a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for comprehensive determination of twelve organophosphate (OP) triesters, five OP diesters and two hydroxylated degradation products in sediment. As the target compound possess a wide range of physicochemical properties, different LC-MS/MS conditions and sample preparation strategies were tested. The optimal condition is based on the extraction of 2 g of dried sediment by ultrasonic-assisted extraction and clean-up by solid phase extraction, and then the extract was separated using a ZORBAX C18 column (4.6 mm × 100 mm, 1.8 μm) and analyzed by MS in multiple reaction monitoring mode. The overall method was validated in terms of linearity, matrix effect, and limits of quantification (LOQs), recoveries and precision. All targets had wide concentration ranges and the correlation coefficients (r) were higher than 0.99. LOQs of all analytes were 0.01-5.0 ng g-1 dw, most of which are lower than those previously reported. In most cases, the recoveries were from 68.56 to 140.22% at three spiked levels (low, medium and high), with RSDs lower than 22.38%, and the reproducibility obtained in five nonconsecutive days was lower than 26.18%. This method was successfully applied to nineteen marine sediment samples. Tri-n-butyl phosphate (TNBP) and tris (phenyl) phosphate (TPHP) were detected in over 84% of samples and the concentration levels were the highest among all OP triesters. For OP diesters, DPHP was 100% detected in all samples with the highest amount. The total concentrations for OP triesters and their degradation products were n.d.-107.2 ng g-1 dw and n.d.-101.7 ng g-1 dw, respectively. This is the first study reporting contamination of both OP triesters and their degradation products, especially hydroxylated degradation products, in sediment. Considering the ubiquitous existence of targets as well as their toxicity to biota, study on the OPEs and their degradation products in marine environment deserves a special attention.
    Keywords:  Degradation products; Liquid chromatography-tandem mass spectrometry (LC-MS/MS); Organophosphate esters (OPEs); Sediment; Ultrasonic-assisted extraction (UAE)