bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2020‒07‒05
eighteen papers selected by
Sofia Costa
Cold Spring Harbor Laboratory

  1. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Jun 20. pii: S1570-0232(20)30220-8. [Epub ahead of print]1152 122252
      Endogenous cannabinoids are an increasingly intriguing target for biological research, given the changing legal status of medicinal cannabinoid-based products throughout the world. However, studying the endogenous cannabinoid system is a relatively new field, with few research teams attempting to develop quantitative methods for these important modulatory analytes in human matrices, other than blood. Here we develop and validate simultaneous methods for quantifying arachidonoyl-ethanolamide, 2-arachidonoyl glycerol, oleoylethanolamide, cortisol and progesterone in human plasma and saliva using liquid-liquid extraction combined with ultra-high performance liquid chromatography coupled to tandem mass spectrometry. The method was fully validated over the linear concentration range 1-20 ng/mL for each analyte in plasma (R2 = 0.98-0.99) and saliva (R2 = 0.99). We find that salivary endogenous cannabinoids and cortisol are acutely responsive to exercise, suggesting that targeting the saliva system may present a convenient way for future research of endogenous cannabinoids. This finding also encourages a broader understanding of the endogenous cannabinoid system during stress responses, and our method may consequently lead to a better understanding of the role of endogenous cannabinoids in peripheral tissues.
    Keywords:  Endocannabinoids; Liquid-liquid extraction; Mass spectrometry; Saliva; Steroids
  2. Methods Mol Biol. 2020 ;2156 203-239
      This book chapter describes the analytical procedures required for the profiling of a metabolite fraction enriched for primary metabolites. The profiling is based on routine gas chromatography coupled to mass spectrometry (GC-MS). The generic profiling method is adapted to plant material, specifically to the analysis of plant material that was exposed to temperature stress. The method can be combined with stable isotope labeling and tracing experiments and is equally applicable to preparations of plant material and microbial photosynthetic organisms. The described methods are modular and can be multiplexed, that is, the same sample or a paired identical backup sample can be analyzed sequentially by more than one of the described procedures. The modules include rapid sampling and metabolic inactivation protocols for samples in a wide weight range, sample extraction procedures, chemical derivatization steps that are required to make the metabolite fraction amenable to gas chromatographic analysis, routine GC-MS methods, and procedures of data processing and data mining. A basic and extendable set of standardizations for metabolite recovery and retention index alignment of the resulting GC-MS chromatograms is included. The methods have two applications: (1) The rapid screening for changes of relative metabolite pools sizes under temperature stress and (2) the verification by exact quantification using GC-MS protocols that are extended by internal and external standardization.
    Keywords:  Absolute quantification; GC-MS; Gas chromatography; Metabolism; Metabolite profiling; Metabolomics; Relative quantification; Stable isotope labeling; TOF-MS; Time-of-flight mass spectrometry
  3. Anal Chem. 2020 Jul 02.
      Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a Buffer Modification Workflow (BMW), in which the same sample is run by LC-MS in both liquid chromatography solvent with 14NH3-acetate buffer, and in solvent with the buffer modified with 15NH3-formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Overall, it identified 26% of ~ 27,000 liver LC-MS features as putative metabolites, of which ~ 2600 showed HMDB or KEGG database formula match. This workflow is well-suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.
  4. Arh Hig Rada Toksikol. 2020 Mar 01. pii: aiht-2020-71-3292. [Epub ahead of print]71(1): 48-55
      Diazinon poisoning is an important issue in occupational, clinical, and forensic toxicology. While sensitive and specific enough to analyse diazinon in biological samples, current methods are time-consuming and too expensive for routine analysis. The aim of this study was therefore to design and validate a simple dispersive liquid-liquid microextraction (DLLME) for the preparation of urine samples to be analysed for diazinon with high performance liquid chromatography with diode-array detector (HPLC-DAD) to establish diazinon exposure and poisoning. To do that, we first identified critical parameters (type and volume of extraction and disperser solvents, pH, surfactant, and salt concentrations) in preliminary experiments and then used central composite design to determine the best experimental conditions for DLLME-HPLC-DAD. For DLLME they were 800 µL of methanol (disperser solvent) and 310 µL of toluene (extraction solvent) injected to the urine sample rapidly via a syringe. The sample was injected into a HPLC-DAD (C18 column, 250×4.6 mm, 5 μm), and the mobile phase was a mixture of acetonitrile and buffer (63:37 v/v, pH 3.2; flow rate: 1 mL/ min). Standard calibration curves for diazinon were linear with the concentration range of 0.5-4 µg/mL, yielding a regression equation Y=0.254X+0.006 with a correlation coefficient of 0.993. The limit of detection and limit of quantification for diazinon were 0.15 µg/mL and 0.45 µg/mL, respectively. The proposed method was accurate, precise, sensitive, and linear over a wide range of diazinon concentrations in urine samples. This method can be employed for diazinon analysis in routine clinical and forensic toxicology settings.
    Keywords:  Taguchi orthogonal array; disperser solvent; extraction solvent; high performance liquid chromatography; liquid phase microextraction
  5. Anal Chem. 2020 Jun 30.
      Targeted quantitative mass spectrometry metabolite profiling is the workhorse of metabolomics research. Robust and reproducible data is essential for confidence in analytical results and is particularly important with large-scale studies. Commercial kits are now available which use carefully calibrated and validated internal and external standards to provide such reliability. However, they are still subject to processing and technical errors in their use and should be subject to a laboratory's routine quality assurance and quality control measures to maintain confidence in the results. We discuss important systematic and random measurement errors when using these kits and suggest measures to detect and quantify them. We demonstrate how wider analysis of the entire data set alongside standard analyses of quality control samples can be used to identify outliers and quantify systematic trends to improve downstream analysis. Finally, we present the MeTaQuaC software which implements the above concepts and methods for Biocrates kits and other target data sets and creates a comprehensive quality control report containing rich visualization and informative scores and summary statistics. Preliminary unsupervised multivariate analysis methods are also included to provide rapid insight into study variables and groups. MeTaQuaC is provided as an open source R package under a permissive MIT license and includes detailed user documentation.
  6. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Jun 13. pii: S1570-0232(20)30185-9. [Epub ahead of print]1152 122243
      The C11-oxy androgens have been implicated in the progression of many diseases and endocrine-linked disorders, such as polycystic ovarian syndrome (PCOS), congenital adrenal hyperplasia, specifically 21-hydroxylase deficiency (21OHD), castration resistant prostate cancer (CRPC), as well as premature adrenarche. While the C11-oxy C19 steroids have been firmly established in the steroid arena, the C11-oxy C21 steroids are now also of significance. The current study reports on a high-throughput ultra-performance convergence chromatography tandem mass spectrometry (UPC2-MS/MS) method for the separation and quantification of 52 steroids in peripheral serum, which include the C11-oxy C19 and C11-oxy C21 steroids. Fifteen deuterium-labelled steroids were included for absolute quantification, which incorporates steroid extraction efficiency, together with one steroid and four non-steroidal compounds serving as quality controls (QC). The 15 min run-time per sample (16 min injection-to-injection time with an 8-step gradient) quantifies 68 analytes in a 2 µL injection volume. A single chromatographic step simultaneously identifies steroids in the mineralocorticoid, glucocorticoid and androgen pathways in adrenal steroidogenesis, together with steroid metabolites produced in the periphery, presenting an analytical method for the application of screening in vivo clinical samples. This study highlights cross-talk between the C11-oxy steroids, and describes the optimisation of multiple reaction monitoring required to measure steroids accurately. The limit of detection for the steroid metabolites ranged from 0.002 to 20 ng/mL and the limit of quantification from 0.02 to 100 ng/mL. The calibration range for the steroids ranged from 0.002 to 1000 ng/mL and for the QC compounds from 0.075 to 750 ng/mL. The method is fully validated in terms of accuracy (%RSD, <13%), precision (including inter-day variability across a three-day period) (%RSD, <16%), recovery (average 102.42%), matrix effect (ranging from -15.25 to 14.25%) and process efficiency (average 101.79%). The dilution protocol for the steroids, internal standards and QC compounds were validated, while the ion ratios of the steroid metabolites (%RSD, <16%) and QC compounds were monitored and the accuracy bias values (%RSD, <9%) were within acceptable limits. The method was subsequently used to quantify steroid levels in a cohort of healthy women. C11-oxy steroid metabolites produced as intermediates in steroidogenic pathways, together with end-products included in the method can potentially characterise the 11β-hydroxyandrostenedione-, C21- and C11-oxy backdoor pathways in vivo. The identification of these C11-oxy C19 and C11-oxy C21 intermediates would allow insight into active pathways, while steroid metabolism could be traced in patients and reference ranges established in both normal and abnormal conditions. Furthermore, conditions currently undefined in terms of the C11-oxy steroids would benefit from the analysis provided by this method, while the C11-oxy steroids could be further explored in PCOS, 21OHD, CRPC and adrenarche.
    Keywords:  11keto-testosterone (11KT); 11β-hydroxyandrostenedione (11OHA4); Castration resistant prostate cancer (CRPC); Congenital adrenal hyperplasia (CAH); Oxygenated; Polycystic ovary syndrome (PCOS)
  7. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2020 Jul 03. 1-14
      A method for simultaneous determination of multi-class antibiotics and steroid hormone analysis in faeces of livestock and poultry was developed using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF MS). An in-house database was built for 156 detected drugs using Personal Compound Database Library software (PCDL) including compound name, monoisotopic mass, chemical formula, RT, chemical structure and three CID MS/MS spectra. The linearity result showed that all the drugs exhibited good linearity with determination coefficients (R2) higher than 0.99. The drug recoveries and their RSDs for all three faeces samples (pig, cattle and chicken) were tested and 81, 96 and 92 drugs were chosen for analysis in pig, cattle and chicken faeces, respectively. Further validation showed that 73 veterinary drugs in all three kinds of faeces samples can be quantified in one analytical run. This work shows that qualitative and quantitative analysis using LC-QTOF MS represents a simple, sensitive, low-cost and high-throughput methodology in routine laboratory analyses.
    Keywords:  Time-of-flight mass spectrometry; antibiotics; livestock and poultry faeces; quantitative analysis; steroid hormones
  8. Front Cell Dev Biol. 2020 ;8 385
      One of the challenges in the area of diagnostics of human thyroid cancer is a preoperative diagnosis of thyroid nodules with indeterminate cytology. Herein, we report an untargeted metabolomics analysis to identify circulating thyroid nodule metabolic signatures, to find new novel metabolic biomarkers. Untargeted gas chromatography-quadrupole-mass spectrometry was used to ascertain the specific plasma metabolic changes of thyroid nodule patients, which consisted of papillary thyroid carcinoma (PTC; n = 19), and multinodular goiter (MNG; n = 16), as compared to healthy subjects (n = 20). Diagnostic models were constructed using multivariate analyses such as principal component analysis, orthogonal partial least squares-discriminant analysis, and univariate analysis including One-way ANOVA and volcano plot by MetaboAnalyst and SIMCA software. Because of the multiple-testing issue, false discovery rate p-values were also computed for these functions. A total of 60 structurally annotated metabolites were subjected to statistical analysis. A combination of univariate and multivariate statistical analyses revealed a panel of metabolites responsible for the discrimination between thyroid nodules and healthy subjects, with variable importance in the projection (VIP) value greater than 0.8 and p-value less than 0.05. Significantly altered metabolites between thyroid nodules versus healthy persons are those associated with amino acids metabolism, the tricarboxylic acid cycle, fatty acids, and purine and pyrimidine metabolism, including cysteine, cystine, glutamic acid, α-ketoglutarate, 3-hydroxybutyric acid, adenosine-5-monophosphate, and uracil, respectively. Further, sucrose metabolism differed profoundly between thyroid nodule patients and healthy subjects. Moreover, according to the receiver operating characteristic (ROC) curve analysis, sucrose could discriminate PTC from MNG (area under ROC curve value = 0.92). This study enhanced our understanding of the distinct metabolic pathways associated with thyroid nodules, which enabled us to distinguish between patients and healthy subjects. In addition, our study showed extensive sucrose metabolism in the plasma of thyroid nodule patients, which provides a new metabolic signature of the thyroid nodule's tumorigenesis. Accordingly, it suggests that sucrose can be considered as a circulating biomarker for differential diagnosis between malignancy and benignity in indeterminate thyroid nodules.
    Keywords:  GC-MS; metabolomics; multinodular goiter; papillary thyroid cancer; thyroid nodules
  9. Ther Drug Monit. 2020 Jun 29.
      BACKGROUND: The combination of trimethoprim (TMP) and sulfamethoxazole (SMX) is used to treat a number of bacterial infections. TMP/SMX concentrations in serum are conventionally monitored using high-performance liquid chromatography (HPLC) or liquid chromatography tandem mass spectrometry (LC-MS/MS). These methods require laborious manual extraction techniques and relatively long sample analysis times, necessitating the development of a simple, high-throughput method. A simple, high-throughput method to measure TMP/SMX using ultra-fast solid-phase extraction-tandem mass spectrometry (SPE-MS/MS) has been developed.METHODS: Calibration standards, quality control materials, and patient samples were precipitated with acetonitrile containing isotopically labeled internal standards. Samples were vortexed, centrifuged for 5 minutes at 2053×g, and the resulting supernatant diluted in aqueous mobile phase and injected onto the C18 SPE cartridge. MS/MS analysis was carried out by electrospray ionization in positive ion mode at a rate of <20 seconds per sample. A five-point linear 1/x calibration curve was used to calculate sample concentrations.
    RESULTS: The intra-assay precision coefficients of variation (PCVs) were <6% and <7% for SMX and TMP, respectively, and <10% for both inter-assay PCVs. Comparison studies using 50 patient and spiked serum samples showed r values of 0.9890 and 0.9853 and y-intercept values of -1.918 and -1.357, respectively compared to the HPLC reference method. All data points were <+/-15% of the mean. Linearity (r = 0.9952 (SMX) and 0.9954 (TMP)) was established from 12 to 400 μg/mL with a detection limit of 0.47 μg/mL, and 1.2 to 40 μg/mL with a detection limit of 0.06 μg/mL, for SMX and TMP, respectively. For either drug, no significant carryover was observed after samples at the upper limit of quantification. No interference was observed from any of the 77 drugs and respective metabolites tested.
    CONCLUSION: A high-throughput SPE-MS/MS method for TMP/SMX quantification was developed. The <20 second analysis time is a significant improvement compared to traditional HPLC and LC-MS/MS methods, without sacrificing analytical performance.
  10. J Biosci Bioeng. 2020 Jun 29. pii: S1389-1723(20)30231-0. [Epub ahead of print]
      Fast enantiomeric separation of amino acids was studied by liquid chromatography/mass spectrometry (LC/MS) on a chiral crown ether stationary phase. A chiral crown ether bonded silica column (3 mm internal diameter (i.d.), 5 cm long) packed with 3 μm particles was employed instead of a 15 cm column packed with 5 μm particles used in our previous study. In addition, the extra-column variance, becoming more serious for smaller columns, was reduced by replacing 0.127 mm i.d. post-column tubes with shorter, smaller-diameter (0.0635 mm i.d.) tubes. The results demonstrated the benefits of using shorter columns packed with smaller particles and the reduction of the extra-column band broadening for fast enantiomeric separation. Finally, the enantiomeric separation of 18 pairs of proteinogenic amino acids was achieved within 2 min with a resolution (Rs) > 1.5 for each pair using an isocratic mobile phase of acetonitrile/water/trifluoroacetic acid (ACN/W/TFA) = 96/4/0.5, and a flow rate 1.2 mL/min at 30°C. This is the highest throughput method for simultaneous chiral separation of all proteinogenic amino acids except proline to date.
    Keywords:  Crown ether; Extra-column effect; Fast enantiomeric separations; Liquid chromatography/time of flight mass spectrometry; d-Amino acids
  11. Gen Comp Endocrinol. 2020 Jun 26. pii: S0016-6480(20)30296-3. [Epub ahead of print] 113543
      Quantification of steroid hormones in fish is an important step for toxicology and endocrinology studies. Among the hormone analysis techniques, liquid chromatography tandem mass spectrometry (LC-MS/MS) has widely been used for measuring hormones in various biological samples. Despite all improvements in the technique, detection of several hormones in a low volume of serum or plasma is still challenging. We developed a robust method for simultaneous quantification of 14 steroid hormones including corticosterone, cortisol, 11-ketotestosterone, progesterone, testosterone, 17OH-progesterone, aldosterone, dihydrotestosterone, estrone, 17β-estradiol, estriol, ethinylestradiol, levonorgestrel and equilin from volumes as low as 10 µL serum or plasma in a short run by LC-MS/MS. The lowest limit of detection in 10 µL serum was 0.012 ng/mL measured for cortisol, progesterone, testosterone, 17OH-progesterone and estrone. Use of high (25 times more) serum volume improved detection limit of hormones by 2-40 times. The method was compared with the radioimmunoassay technique in which testosterone and 17β-estradiol were highly correlated with R2 of 0.95 and 0.96, respectively. We validated the method by measuring four selected hormones, in low and high plasma volumes of largemouth bass (Micropterus salmoides). In addition, we developed a method to quantify hormones in whole body fish homogenates of small fish and compared the values to plasma concentrations, using fathead minnow (Pimephales promelas). Calculated concentrations of the hormones in plasma were consistent with those in the homogenate and 11-ketotestosterone and 17β-estradiol were significantly different in males and females. The ability to measure hormones from whole body homogenates was further evaluated in two model small fish species, zebrafish (Danio rerio) and juvenile silverside (Menidia beryllina). These results suggest that whole tissue homogenate is a reliable alternative for hormone quantification when sufficient plasma is not available.
    Keywords:  Fish; LC-MS/MS; Plasma; Steroid hormone
  12. Int J Mol Sci. 2020 Jun 26. pii: E4568. [Epub ahead of print]21(12):
      Current methods for the intraoperative determination of breast cancer margins commonly suffer from the insufficient accuracy, specificity and/or low speed of analysis, increasing the time and cost of operation as well the risk of cancer recurrence. The purpose of this study is to develop a method for the rapid and accurate determination of breast cancer margins using direct molecular profiling by mass spectrometry (MS). Direct molecular fingerprinting of tiny pieces of breast tissue (approximately 1 × 1 × 1 mm) is performed using a home-built tissue spray ionization source installed on a Maxis Impact quadrupole time-of-flight mass spectrometer (qTOF MS) (Bruker Daltonics, Hamburg, Germany). Statistical analysis of MS data from 50 samples of both normal and cancer tissue (from 25 patients) was performed using orthogonal projections onto latent structures discriminant analysis (OPLS-DA). Additionally, the results of OPLS classification of new 19 pieces of two tissue samples were compared with the results of histological analysis performed on the same tissues samples. The average time of analysis for one sample was about 5 min. Positive and negative ionization modes are used to provide complementary information and to find out the most informative method for a breast tissue classification. The analysis provides information on 11 lipid classes. OPLS-DA models are created for the classification of normal and cancer tissue based on the various datasets: All mass spectrometric peaks over 300 counts; peaks with a statistically significant difference of intensity determined by the Mann-Whitney U-test (p < 0.05); peaks identified as lipids; both identified and significantly different peaks. The highest values of Q2 have models built on all MS peaks and on significantly different peaks. While such models are useful for classification itself, they are of less value for building explanatory mechanisms of pathophysiology and providing a pathway analysis. Models based on identified peaks are preferable from this point of view. Results obtained by OPLS-DA classification of the tissue spray MS data of a new sample set (n = 19) revealed 100% sensitivity and specificity when compared to histological analysis, the "gold" standard for tissue classification. "All peaks" and "significantly different peaks" datasets in the positive ion mode were ideal for breast cancer tissue classification. Our results indicate the potential of tissue spray mass spectrometry for rapid, accurate and intraoperative diagnostics of breast cancer tissue as a means to reduce surgical intervention.
    Keywords:  breast cancer; direct mass spectrometry; discriminant model; lipidomics; molecular profiling; tissue spray
  13. Biomed Chromatogr. 2020 Jun 30. e4936
      Acamprosate is a medication used to treat alcohol dependence. Therapeutic drug monitoring is important in drugs for the treatment of substance-related disorders. Therefore, in this study, a new selective, very simple, and rapid ultra-performance liquid chromatography-tandem mass spectrometer method was developed for the therapeutic drug monitoring of acamprosate. The developed method allows the determination of acamprosate in human plasma. The method was validated in terms of selectivity and linearity, which was in the range of 100-1200 ng/mL for acamprosate. Intra-assay and inter-assay accuracy and precision were found within acceptable limits of the EMA guideline. The lower limit of quantitation was 100 ng/mL for acamprosate. The developed method was successfully applied for therapeutic drug monitoring in the patient's plasma samples.
    Keywords:  Acamprosate; Therapeutic drug monitoring; UPLC-MS/MS; bioanalytical method validation; human plasma
  14. Anal Chem. 2020 Jun 30.
      The present research reports on the development of a methodology to unravel the complex phytochemistry of cannabis. Specifically, cannabis inflorescences were considered and stir bar sorptive extraction (SBSE) was used for pre-concentration of the metabolites. Analytes were thermally-desorbed into a comprehensive two-dimensional gas chromatography (GC×GC) system coupled with low- and high-resolution mass spectrometry (MS). Particular attention was devoted to the optimization of the extraction conditions to extend the analytes' coverage, and to the optimization of the chromatographic separation to obtain a robust dataset for further untargeted analysis. Monoterpenes, sesquiterpenes, hydrocarbons, cannabinoids, other terpenoids, and fatty acids were considered to optimize the extraction conditions. The response of selected ions for each chemical class, delimited in specific 2D chromatographic regions, enabled an accurate and fast evaluation of the extraction variables (i.e., time, temperature, solvent, salt addition), which were then selected to have a wide analyte selection and good reproducibility. Under optimized SBSE conditions, eight different cannabis inflorescences, and a quality control sample were analyzed and processed following an untargeted and unsupervised approach. Principal component analysis on all detected metabolites revealed chemical differences among the sample types which could be associated with the plant subspecies. With the same SBSE-GC×GC-MS methodology, a quantitative targeted analysis was performed on three common cannabinoids, namely delta-9-tetrahydrocannabinol, cannabidiol, and cannabinol. The method was validated, giving correlation fac-tors over 0.993, and <12% reproducibility (relative standard deviation) at the lowest calibration point. The high-resolution MS acquisition allowed for high confidence identification and post-targeted analysis, confirming the presence of two pesticides, a plasticizer, and a cannabidiol degradation product in some of the samples.
  15. Sci Rep. 2020 Jul 02. 10(1): 10918
      There is a long-standing concern for the lack of reproducibility of the untargeted metabolomic approaches used in pharmaceutical research. Two types of human plasma samples were split into two batches and analyzed in two individual labs for untargeted GC-MS metabolomic profiling. The two labs used the same silylation sample preparation protocols but different instrumentation, data processing software, and database. There were 55 metabolites annotated reproducibly, independent of the labs. The median coefficient variations (CV%) of absolute spectra ion intensities in both labs were less than 30%. However, the comparison of normalized ion intensity among biological groups, were inconsistent across labs. Predicted power based on annotated metabolites was evaluated post various normalization, data transformation and scaling. For the first time our study reveals the numerical details about the variations in metabolomic annotation and relative quantification using plain inter-laboratory GC-MS untargeted metabolomic approaches. Especially we compare several commonly used post-acquisition strategies and found normalization could not strengthen the annotation accuracy or relative quantification precision of untargeted approach, instead it will impact future experimental design. Standardization of untargeted metabolomics protocols, including sample preparation, instrumentation, data processing, etc., is critical for comparison of untargeted data across labs.
  16. Anal Chem. 2020 Jul 01.
      A major challenge for Metabolomic analysis is to obtain an unambiguous identification of the metabolites detected in a sample. Among metabolomics techniques, NMR spectroscopy is a sophisticated, powerful, and generally applicable spectroscopic tool that can be used to ascertain the correct structure of newly isolated biogenic molecules. However, accurate structure prediction using computational NMR techniques depends on how much of the relevant conformational space of a particular compound is considered. It is intrinsically challenging to calculate NMR chemical shifts using high-level DFT when the conformation-al space of a metabolite is extensive. In this work, we developed NMR chemical shift calculation protocols using a machine learning model in conjunction with standard DFT methods. The pipeline encompasses the following steps: (1) conformation generation using a force field (FF) based method, (2) filtering the FF generated conformations using the ASE-ANI machine learning model, (3) clustering of the optimized conformations based on structural similarity to identify chemically unique conformations, (4) DFT structural optimization of the unique conformations and (5) DFT NMR chemical shift calculation. This protocol can calculate the NMR chemical shifts of a set of molecules using any available combination of DFT theory, solvent model, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Our protocol reduces the overall computational time by 2 orders of magnitude (see Figure 1) over methods that optimize the conformations using fully ab initio methods, while still producing good agreement with experimental observations. The complete protocol is designed in such a manner that makes the computation of chemical shifts tractable for a large number of conformationally flexible metabolites.
  17. J Am Soc Mass Spectrom. 2020 Jul 02.
      Squamous intraepithelial lesion is an abnormal growth of epithelial cells on the surface of the cervix that may lead to cervi-cal cancer. Analytical protocols for the determination of squamous intraepithelial lesions are highly demanded since cervical cancer is the fourth most diagnosed cancer among women in the world. Here, paper spray ionization mass spectrometry (PSI-MS) is used to distinguish between healthy (negative for intraepithelial lesion or malignancy) and diseased (high-grade squamous intraepithelial lesion) blood plasmas. A total of 86 blood samples of different women (healthy = 49 samples; diseased = 37 samples) were collected, and the plasmas were prepared. Then, 10 µL of each plasma sample was deposited onto triangular papers for PSI-MS analysis. No additional step of sample preparation was necessary. The interval-successive projection algorithm linear discriminant analysis (iSPA-LDA) was applied to the PSI mass spectra, showing six ions (mostly phospholipids) that were predictive of healthy and diseased plasmas. Values of 77% of accuracy, 86% of sensitivity, 80% of PPV, and 75% of NPV were achieved. This study provides evidence that PSI-MS may potentially be used as a fast and simple analytical technique for early diagnosis of cervical cancer.
  18. J Chromatogr Sci. 2020 Jun 29. pii: bmaa027. [Epub ahead of print]
      A precise, swift and environmental-friendly reverse phase ultra-high performance liquid chromatographic assay for the determination of thymoquinone (TQ) in plasma samples using thymol (TM) as an internal standard was developed and validated. The method used a high strength silica C18 1.7 μm column (100 × 2.1 mm) with an isocratic mobile phase consisting of a blend of methanol and 20 mM potassium dihydrogen ortho-phosphate (90:10 v/v; pH of 4.2). The selected eluent provided a short run time (≤2 min), better peak symmetry, lower limit of quantification of 10 ng/mL and satisfactory values of other chromatographic parameters including resolution (Rs = 1), capacity factor (k = 21.5 and 14.5 for TQ and TM, respectively), selectivity (α = 1.482) and number of theoretical plates (N = 1653 and 784 for TQ and TM, respectively). The method was efficiently applied to a pharmacokinetic study of TQ following an intraperitoneal administration of 2 mg/kg in mice. The concentrations of TQ in plasma were measurable up to 12 h with Cmax of 404.08 ± 28.91 ng/mL, T1/2 of 2.31 ± 0.10 h and area under plasma concentration-time curve of 1527.00 ± 46.61 ng/mL × h.