bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2020‒03‒15
thirty-four papers selected by
Sofia Costa
Cold Spring Harbor Laboratory


  1. Anal Chem. 2020 Mar 09.
    Wijnant K, Van Meulebroek L, Pomian B, De Windt K, De Henauw S, Michels N, Vanhaecke L.
      Whereas urine and blood are typically targeted in clinical research, saliva represents an interesting alternative as its intrinsic metabolome is chemically diverse and reflective for various biological processes. Moreover, saliva collection is easy and non-invasive, which is especially valuable for cohorts in which sample collection is challenging, e.g. infants and children. With this rationale, we established a validated UHPLC-HRMS method for salivary metabolic profiling and fingerprinting. Hereby, 450 μL of saliva was centrifuged and passed over a 0.45-μm polyamide membrane filter, after which the extract was subjected to chromatographic analysis (HSS T3 column) and Q-ExactiveTM Orbitrap-MS. For the majority of the profiled metabolites, good linearity (R2 ≥ 0.99) and precision (coefficient of variance ≤ 15%) was achieved. The fingerprinting performance was evaluated based on the complete metabolome (11,385 components), whereby 76.8% was found compliant with the criteria for precision (coefficient of variance ≤ 30%) and 82.7% with linearity (R2 ≥ 0.99). In addition, the method was proven fit-for-purpose for a cohort of 140 adolescents (6-16 years, stratified according to weight), yielding relevant profiles (45 obesity-related metabolites) and discriminative fingerprints (Q2 of 0.784 for supervised discriminant analysis). Alternatively, LA-REIMS was established for rapid fingerprinting of saliva, thereby using a Nd:YAG laser and Xevo G2-XS QToF-MS. With an acquisition time of 0.5 min per sample, LA-REIMS offers unique opportunities for point-of-care applications. In conclusion, this work presents a platform of UHPLC-HRMS and LA-REIMS, complementing each other to perform salivary metabolomics.
    DOI:  https://doi.org/10.1021/acs.analchem.9b05598
  2. J Chromatogr A. 2020 Feb 26. pii: S0021-9673(20)30205-3. [Epub ahead of print] 460999
    Duan L, Ma A, Meng X, Shen GA, Qi X.
      Gas chromatography-mass spectrometry (GC-MS) is a robust analytical platform for analysis of small molecules. Recently, it is widely used for large-scale metabolomics studies, in which hundreds or even thousands of samples are analyzed simultaneously, producing a very large and complex GC-MS datasets. A number of software are currently available for processing GC-MS data, but it is too compute-intensive for them to efficiently and accurately align chromatographic peaks from thousands of samples. Here, we report a newly developed software, QPMASS, for analysis of large-scale GC-MS data. The parallel computing with an advanced dynamic programming approach is implemented in QPMASS to align peaks from multiple samples based on retention time and mass spectra, enabling fast processing large-scale datasets. Furthermore, the missing value filtering and backfilling are introduced into the program, greatly reducing false positive and false negative errors to be less than 5%. We demonstrated that it took only 8 h to align and quantify a GC-TOF-MS dataset from 300 rice leaves samples, and 17 h to process a GC-qMS dataset from 1000 rice seed samples by using a personal computer (3.70 GHz CPU, 16 GB of memory and > 100 GB hard disk). QPMASS is written in C++ programming language, and is able to run under Windows operation system with a user-friendly interface.
    Keywords:  Data analysis; GC-MS; Metabolomics; Parallel computing; QPMASS
    DOI:  https://doi.org/10.1016/j.chroma.2020.460999
  3. J Proteome Res. 2020 Mar 13.
    Mohamed A, Molendijk J, Hill MM.
      The rapid evolution of mass spectrometry (MS)-based lipidomics has enabled the simultaneous measurement of numerous lipid classes. With lipidomics datasets becoming increasingly available, lipidomic-focused software tools are required to facilitate data analysis as well as mining of public datasets, integrating lipidomics-unique molecular information, such as lipid class, chain length and unsaturation. To address this need, we developed lipidr, an open-source R/Bioconductor package for data mining and analysis of lipidomics datasets. lipidr implements a comprehensive lipidomic-focused analysis workflow for targeted and untargeted lipidomics. lipidr imports numerical matrices, Skyline exports and Metabolomics Workbench files directly into R, automatically inferring lipid class and chain information from lipid names. Through integration with the Metabolomics Workbench API, users can search, download and reanalyze public lipidomics datasets seamlessly. lipidr allows thorough data inspection, normalization, uni- and multivariate analyses, displaying results as interactive visualizations. To enable interpretation of lipid class, chain length and total unsaturation data, we also developed and implemented a novel Lipid Set Enrichment Analysis. A companion online guide with two live example datasets is presented at https://www.lipidr.org/.We expect that the ease of use and innovative features of lipidr allow the lipidomics research community to gain novel detailed insights from lipidomics data.
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00082
  4. J Sep Sci. 2020 Mar 12.
    Fragkaki AG, Petropoulou G, Athanasiadou I, Kiousi P, Kioukia-Fougia N, Archontaki H, Bakeas E, Angelis YS.
      Anabolic androgenic steroids are widely abused substances in sports doping. Their detection present limitations regarding the use of soft ion sources such as electrospray or atmospheric pressure chemical ionization by LC-MS/MS. In the current study, a novel derivatization method was developed for the ionization enhancement of selected anabolic androgenic steroids. The proposed method aims at the introduction of an easily ionizable moiety into the steroid molecule by converting the hydroxyl groups into imidazole carbamates using 1,1'-carbonyldiimidazole as derivatization reagent. The proposed method was applied to water and urine samples spiked with exogenous anabolic androgenic steroids in various concentration levels. Steroid imidazole carbamate derivatives have shown intensive [M+H]+ signals under electrospray ionization and common fragmentation patterns in MS/MS mode with [M-CO2 +H]+ and [M-ΙmCO2 +H]+ as major ions with low collision energy. The obtained results showed that the majority of steroids were detectable at concentrations equal or lower to their Minimum Required Performance Level according to the World Anti-Doping Agency technical document. The proposed method is sensitive with a preparation procedure that could be easily applied to the analysis of doping control samples. This article is protected by copyright. All rights reserved.
    Keywords:  Anabolic androgenic steroids; derivatization; doping control; imidazole carbamates; mass spectrometry
    DOI:  https://doi.org/10.1002/jssc.202000036
  5. Anal Chem. 2020 Mar 13.
    Kostyukevich YI, Zherebker AY, Orlov A, Kovaleva O, Burykina T, Isotov B, Nikolaev EN.
      Accurate and reliable identification of chemical compounds is the ultimate goals of the mass spectrometry analyses. Currently identification of compounds is usually based on the measurement of accurate mass and fragmentation spectrum, chromatographic elution time, collisional cross-section. Unfortunately, despite the growth of databases of experimentally measured MS/MS spectra (such as MzCloud, Metlin etc.) and developing software for predicting MS/MS fragments in silico from SMILES patters (such as MetFrag, CFM-ID, Ms-Finder etc.) the problem of identification is still unsolved. The major issue is that the elution time and fragmentation spectra depend considerably on the equipment used and are not the same for different LC-MS systems. It means that any additional descriptors depending only on the structure of the chemical compound will be of the big help for LC-MS/MS based omics. Our approach is based on the characterization of compounds by the number of labile hydrogens and oxygens atoms in the molecule which can be measured using Hydrogen/Deuterium and 16O/18O exchange approaches. The number of labile atoms (those from -OH, -NH, =O, -COOH groups) can be predicted from SMILES patterns and serves as an additional structural descriptor when performing database search. In addition, distribution of isotope labels among MS/MS fragments can be roughly predicted by software such as MetFrag or CFM-ID. Here we present an approach utilizing the selection of structural candidates from database based on the number of functional groups and analysis of isotope labels distribution among fragments. It was found that our approach allows reducing of the search space by the factor of 10 and considerably increases the reliability of the compound identification.
    DOI:  https://doi.org/10.1021/acs.analchem.9b05379
  6. Biomed Chromatogr. 2020 Mar 12. e4826
    Yi X, Lan X.
      Erianin is one of the bibenzyl ingredients isolated from Dctidrobium chrysotoxum Lindl. In recent years, erianin has attracted attention due to its anti-tumor activity. In this study, an LC-MS/MS method was established to measure erianin in rat plasma. Gigantol was used as the internal standard. A Waters ACQUITY UPLC BEH C18 column was employed for chromatographic separation. The mobile phase consisted of water containing 0.1% formic acid and acetonitrile with a gradient elution at the flow rate of 0.4 mL/min. Selective reaction monitoring (SRM) mode was used for quantitative analysis of erianin in positive electrospray ionization. In the concentration range of 0.1-1200 ng/mL, erianin in rat plasma was linear with correlation coefficient > 0.999. The lowest limit of quantification was 0.1 ng/mL. The intra- and inter-day RSD% were less than 9.69%, while the RE% was in the range of -8.59-11.24%. The mean recovery was >85.37%. Erianin was stable in rat plasma after storage at certain conditions. The validated method was demonstrated to be selective, sensitive and reliable, which has been successfully applied to pharmacokinetic study of erianin in rat plasma. Erianin was rapidly eliminated from rat plasma with s short half-life (⁓1.5 h) and low oral bioavailability (8.7%).
    Keywords:  Erianin; bioavailability; liquid chromatography tandem mass spectrometry; pharmacokinetics; rats
    DOI:  https://doi.org/10.1002/bmc.4826
  7. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Feb 24. pii: S1570-0232(19)31628-9. [Epub ahead of print]1142 122041
    Guan Y, Deng Q, Li G, Si L, Long L, Soleimani Damaneh M, Huang J.
      Obesity has become a severe public health problem worldwide. An endogenous fatty acid ethanolamine oleoyl ethanolamine (OEA) is reported to be capable of reducing body weight and food intake by increasing striatal extracellular dopamine concentration. However, association between obesity and striatal OEA level remains unknown. As such, it is necessary to develop a sensitive and reliable method to quantitate OEA concentration in striatum. Because true endogenous analytes free blank matrix is not available, surrogate analyte, surrogate matrix and background subtraction methods are often employed for the analysis of endogenous compounds. In this study, three liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods were developed and validated for the determination of OEA concentration in mouse brain homogenate. Interestingly, stability results found that OEA-d4 degraded in brain homogenate under room temperature, while OEA level remarkably increased with time. Since lowering temperature could observably decelerate the endogenous transformation of OEA, sample collection and preparation were carried out under ice-bath condition. Hexane: isopropanol (9:1, v/v) was employed as an extractant for liquid-liquid extraction. After method validation, three methods were applied to quantify OEA in striatum homogenate from C57B6/L mice following normal and high fat diet feeding for 4 months. Results from three methods all showed the striatal OEA level in obesity group was significantly higher than control group and obesity-resist group, which indicated that obesity might be associated with elevated striatal OEA level.
    Keywords:  Comparison; LC-MS/MS; Obesity; Oleoyl ethanolamine; Striatum
    DOI:  https://doi.org/10.1016/j.jchromb.2020.122041
  8. Molecules. 2020 Mar 10. pii: E1254. [Epub ahead of print]25(5):
    Choi WG, Kim DK, Shin Y, Park R, Cho YY, Lee JY, Kang HC, Lee HS.
      Doxorubicin, an anthracycline antitumor antibiotic, acts as a cancer treatment by interfering with the function of DNA. Herein, liquid chromatography-tandem mass spectrometry was for the first time developed and validated for the simultaneous determination of doxorubicin and its major metabolites doxorubicinol, doxorubicinone, doxorubicinolone, and 7-deoxydoxorubicinone in mouse plasma. The liquid-liquid extraction of a 10 μL mouse plasma sample with chloroform:methanol (4:1, v/v) and use of the selected reaction monitoring mode led to less matrix effect and better sensitivity. The lower limits of quantification levels were 0.5 ng/mL for doxorubicin, 0.1 ng/mL for doxorubicinol, and 0.01 ng/mL for doxorubicinone, doxorubicinolone, and 7-deoxydoxorubicinone. The standard curves were linear over the range of 0.5-200 ng/mL for doxorubicin; 0.1-200 ng/mL for doxorubicinol; and 0.01-50 ng/mL for doxorubicinone, doxorubicinolone, and 7-deoxydoxorubicinone in mouse plasma. The intra and inter-day relative standard deviation and relative errors for doxorubicin and its four metabolites at four quality control concentrations were 0.9-13.6% and -13.0% to 14.9%, respectively. This method was successfully applied to the pharmacokinetic study of doxorubicin and its metabolites after intravenous administration of doxorubicin at a dose of 1.3 mg/kg to female BALB/c nude mice.
    Keywords:  7-deoxydoxorubicinone; LC-MS/MS; doxorubicin; doxorubicinol; doxorubicinolone; doxorubicinone; mouse plasma
    DOI:  https://doi.org/10.3390/molecules25051254
  9. J Am Soc Mass Spectrom. 2020 Mar 10.
    Park JM, Kim M, Noh JY, Yun TG, Kang MJ, Lee SG, Yoo BC, Pyun JC.
      Recently, the parylene-matrix chip was developed for quantitative analysis of small molecules less than 1 kDa. In this study, MALDI-TOF MS based on the parylene-matrix chip was performed to clinically diagnose intrahepatic cholangiocarcinoma (IHCC) and colorectal cancer (CRC). The parylene-matrix chip was applied for the detection of small cancer biomarkers including N-methyl-2-pyridone-5-carboxamide (2PY), glutamine, lysophosphatidylcholine (LPC) 16:0 and LPC 18:0. The feasibility of MALDI-TOF MS based on the parylene-matrix chip was confirmed via analysis of spot-to-spot and shot-to-shot reproducibility. Serum metabolite markers of IHCC, N-methyl-2-pyridone-5-carboxamide (2PY) and glutamine, were quantified using MALDI-TOF MS based on the parylene-matrix chip. For clinical diagnosis of CRC, two water-insoluble (barely soluble) biomarkers, lysophosphatidylcholine (LPC) 16:0 and LPC 18:0, were quantified. Finally, glutamine and LPC 16:0 were simultaneously detected at a range of concentrations in sera from colon cancer patients using the parylene-matrix chip. Thus, this method yielded high-throughput detection of cancer biomarkers for the mixture samples of water-soluble analytes (2PY and glutamine) and water-insoluble analytes (LPC 16:0 and LPC 18:0).
    DOI:  https://doi.org/10.1021/jasms.9b00102
  10. Rapid Commun Mass Spectrom. 2020 Mar 10.
    Ory L, Gentil E, Kumla D, Kijjoa A, Nazih EH, Roullier C.
      RATIONALE: In the field of natural products, dereplication of complex mixtures hasbecomes usual practice to annotate known compounds and avoid their re-isolation. To this purpose, many groups rely on liquid chromatography coupled to high resolution mass spectrometry to deduce molecular formulae of compounds allowing comparison with public or in-house databases. Electrospray ionisation is usually considered as the method of choice to investigate a large panel of compounds but, in some cases, it may lead to unusual results as described in the following article for ergosterol.METHODS: Ergosterol and other fungal sterols in methanolic solution were analysed using different chromatographic gradients by HPLC/MS on both IT-TOFMS and Orbitrap-MS instruments fitted with an ESI source. Further flow injection analyses were performed to investigate the influence of the solvent composition. MS/MS fragmentation data were acquired to annotate the different ions observed.
    RESULTS: Contrary to other fungal sterols, ergosterol was found to be highly sensitive to oxidation during electrospray ionisation. Putative structures were proposed based on MS/MS studies and known oxidation mechanisms of ergosterol by reactive oxygen species (ROS) that could be formed in the ESI process. The proportion of acetonitrile in the eluent was found to influence this in-source oxidation, with increased proportion of oxidized sodium adducts with higher proportions of acetonitrile.
    CONCLUSIONS: While ergosterol is a major sterol found in fungi, this study investigates its ionisation by electrospray for the first time. The results reported here will help further detection and annotation of this compound in fungal extracts after HPLC/ESI-MS analyses.
    DOI:  https://doi.org/10.1002/rcm.8780
  11. J Am Soc Mass Spectrom. 2020 Mar 13.
    Wang HJ, Hsu FF.
      Fatty acyl coenzyme A esters (FA-CoAs) are important crossroad intermediates in lipid catabolism and anabolism, and the structures are complicated. Several mass spectrometric approaches have been previously described to elucidate their structures. However, a direct mass spectrometric approach toward a complete identification of the molecule, including the location of unsaturated bond(s) in the fatty acid chain has not been reported. In this study we applied a simple MALDI/TOF mass spectrometric method to a near complete characterization of long-chain FA-CoAs, including the location(s) of the double-bond in the fatty acyl chain, and the common structural features that recognize FA-CoAs. Negative ion mass spectra of saturated, monounsaturated, and polyunsaturated FA-CoAs were acquired with MALDI/TOF mass spectrometer using 2,5-dihydroxybenzoic acid as the matrix and ionized with a laser fluence two folds of the threshold to induce the in-source fragmentation (ISF) of the analytes. The resulting ISF spectra contained fragment ions arising from specific cleavages of the C-C bond immediate adjacent to the acyl double-bond. This structural feature affords locating the double-bond position(s) of the fatty acyl substituent. Thereby, positional isomer such as 18:3(n-3) and 18:3(n-6) FA-CoA can be differentiated without applying tandem mass spectrometry.
    DOI:  https://doi.org/10.1021/jasms.9b00139
  12. Cancers (Basel). 2020 Mar 07. pii: E622. [Epub ahead of print]12(3):
    Zhang L, Zheng J, Ahmed R, Huang G, Reid J, Mandal R, Maksymuik A, Sitar DS, Tappia PS, Ramjiawan B, Joubert P, Russo A, Rolfo CD, Wishart DS.
      The objective of this research is to use metabolomic techniques to discover and validate plasma metabolite biomarkers for the diagnosis of early-stage non-small cell lung cancer (NSCLC). The study included plasma samples from 156 patients with biopsy-confirmed NSCLC along with age and gender-matched plasma samples from 60 healthy controls. A fully quantitative targeted mass spectrometry (MS) analysis (targeting 138 metabolites) was performed on all samples. The sample set was split into a discovery set and validation set. Metabolite concentration data, clinical data, and smoking history were used to determine optimal sets of biomarkers and optimal regression models for identifying different stages of NSCLC using the discovery sets. The same biomarkers and regression models were used and assessed on the validation models. Univariate and multivariate statistical analysis identified β-hydroxybutyric acid, LysoPC 20:3, PC ae C40:6, citric acid, and fumaric acid as being significantly different between healthy controls and stage I/II NSCLC. Robust predictive models with areas under the curve (AUC) > 0.9 were developed and validated using these metabolites and other, easily measured clinical data for detecting different stages of NSCLC. This study successfully identified and validated a simple, high-performing, metabolite-based test for detecting early stage (I/II) NSCLC patients in plasma. While promising, further validation on larger and more diverse cohorts is still required.
    Keywords:  LC-MS; cancer staging; early detection; lung cancer; metabolomics
    DOI:  https://doi.org/10.3390/cancers12030622
  13. Anal Bioanal Chem. 2020 Mar 13.
    Li L, Chen Y, Yang Y, Yang Y, Yang L, Wang Z.
      Progesterone is the representative progestogens in five major classes of steroid hormones and plays important roles in mammalian pregnancy and animal growth and development. Conventional available analytical methods for progesterone involve immunoassay, gas chromatography-mass spectrometry (GC-MS), and high-performance liquid chromatography-mass spectrometry (HPLC-MS), which lack specificity or usually require sophisticated operations and relatively long time. Herein, we developed a novel strategy for rapid analysis of progesterone via direct analysis in real time mass spectrometry (DART-MS) combined with solid-phase extraction (SPE) using an amino functionalized metal-organic frameworks (MOFs). Under optimized conditions, a wide linear range of 0.5-500 ng mL-1 was achieved, with a satisfactory correlation coefficient (R2 = 0.9992). The relative standard deviations (RSDs) were in the range from 2.4 to 8.4%, demonstrating good precision. The applicability was then confirmed by analyzing spiked lake water and synthetic urine samples, and recoveries are between 92.0 and 117.8% in all three spiked levels (5, 25, and 100 ng mL-1). The sensitivity was notably improved compared with solely DART-MS and obtained detection limit decreased by about 50 times. This research provided a rapid, simple, highly sensitive, and efficient approach for analysis of hormones through combination of advantages of ambient mass spectrometry and porous nanomaterials. Graphical abstract.
    Keywords:  Direct analysis in real time mass spectrometry; Metal-organic frameworks; Progesterone; Sample preparation; Solid-phase extraction; Steroid hormones
    DOI:  https://doi.org/10.1007/s00216-020-02535-6
  14. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Feb 24. pii: S1570-0232(19)31754-4. [Epub ahead of print]1142 122040
    Liang X, Xiang Y, Li Y, Feng P, Qin Y, Lai X.
      Berberidis cortex, the dry bark of Berberis L., is used to treat diabetes and contains at least three bioactive components: berberine (BBR), berbamine (BBM) and magnoflorine (MGF). BBR in turn is metabolized into berberrubine (BRB). Although it is possible to quantify each of these components individually in serum, there are currently no methods for simultaneously quantifying all four. Here, we developed a specific and rapid method for simultaneously quantifying BBR, BBM, MGF and BRB in mouse serum using ultra high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Samples were pretreated by protein precipitation, separated using an ACQUITY UPLC® BEH C18 column and detected by a triple quadrupole mass spectrometer with electrospray ionization. The compound [9,10-(OC2H3)2]-BBR (d6-BBR) was used as internal standard for BBR and BRB, boldine (BOL) for MGF and tetrandrine (TET) for BBM. The m/z transitions for precursor/product ion pairs were 336.1/320.2 for BBR, 305.2/566.3 for BBM, 342.0/297.1 for MGF, 322.1/307.2 for BRB, 342.2/294.3 for d6-BBR, 312.2/580.3 for TET and 328.1/265.2 for BOL. We validated our method in terms of selectivity, linearity and lower limit of quantification, accuracy, precision, matrix effect and recovery, dilution integrity and stability. This method showed good linearity from 0.1 to 40 ng/mL for BBR, 8 to 3200 ng/mL for BBM, 5 to 2000 ng/mL for MGF and 0.2 to 80 ng/mL for BRB. The chromatographic run time was 3.9 min, and sample preparation took approximately 15 min per batch. Finally, we used our method to measure BBR, BBM, MGF and BRB in serum from diabetic mice after gavage administration of BBR hydrochloride, BBM hydrochloride, and MGF. This method is precise, accurate and suitable for high-throughput sample analysis.
    Keywords:  Berbamine; Berberidis cortex; Berberine; Berberrubine; Magnoflorine; UPLC-MS/MS
    DOI:  https://doi.org/10.1016/j.jchromb.2020.122040
  15. Anal Chem. 2020 Mar 13.
    Hernández-Mesa M, D'Atri V, Barknowitz G, Fanuel M, Pezzatti J, Dreolin N, Ropartz D, Monteau F, Vigneau E, Rudaz S, Stead S, Rogniaux H, Guillarme D, Dervilly G, Le Bizec B.
      Collision cross section (CCS) databases based on single-laboratory measurements must be cross-validated to extend their use in peak annotation. This work addresses the validation of the first comprehensive TWCCSN2 database for steroids. First, its long-term robustness was evaluated (i.e. a year and a half after database generation; Synapt G2-S instrument; bias within ±1.0% for 157 ions, 95.7% of the total ions). It was further cross-validated by three external laboratories, including two dif-ferent TWIMS platforms (i.e., Synapt G2-Si and two Vion IMS QToF; bias within the threshold of ±2.0% for 98.8, 79.9 and 94.0% of the total ions detected by each instrument, respectively). Finally, a cross-laboratory TWCCSN2 database was built for 87 steroids (142 ions). The cross-laboratory database consists of average TWCCSN2 values obtained by the four TWIMS instruments in triplicate measurements. In general, lower deviations were observed between TWCCSN2 measurements and reference values when the cross-laboratory database was applied as reference instead of the single-laboratory database. Relative standard deviations below 1.5% were observed for inter-laboratory measurements (< 1.0% for 85.2% of ions) and bias between average values and TWCCSN2 measurements was within the range of ±1.5% for 96.8% of all cases. In the con-text of this inter-laboratory study, this threshold was also suitable for TWCCSN2 measurements of steroid metabolites in calve urine. Greater deviations were observed for steroid sulfates in complex urine samples of adult bovines, showing a slight ma-trix effect. The implementation of a scoring system for the application of the CCS descriptor in peak annotation is also discussed.
    DOI:  https://doi.org/10.1021/acs.analchem.9b05247
  16. J Mass Spectrom. 2020 Feb 19. e4506
    Courlet P, Alves Saldanha S, Cavassini M, Marzolini C, Choong E, Csajka C, Günthard HF, André P, Buclin T, Desfontaine V, Decosterd LA.
      The widespread use of highly active antiretroviral treatments has dramatically changed the prognosis of people living with HIV (PLWH). However, such treatments have to be taken lifelong raising issues regarding the maintenance of both therapeutic effectiveness and long-term tolerability. Recently approved or investigational antiretroviral drugs present considerable advantages, allowing once daily oral dosage along with activity against resistant variants (eg, bictegravir and doravirine) and also parenteral intramuscular administration that facilitates treatment adherence (eg, long-acting injectable formulations such as cabotegravir and rilpivirine). Still, there remains a risk of insufficient or exaggerated circulating exposure due to absorption issues, abnormal elimination, drug-drug interactions, and others. In this context, a multiplex ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) bioassay has been developed for the monitoring of plasma levels of bictegravir, cabotegravir, doravirine, and rilpivirine in PLWH. A simple and convenient protein precipitation was performed followed by direct injection of the supernatant into the UHPLC-MS/MS system. The four analytes were eluted in less than 3 minutes using a reversed-phase chromatography method coupled with triple quadrupole mass spectrometry detection. This bioassay was fully validated following international guidelines and achieved good performances in terms of trueness (94.7%-107.5%), repeatability (2.6%-11%), and intermediate precision (3.0%-11.2%) over the clinically relevant concentration ranges (from 30 to 9000 ng/mL for bictegravir, cabotegravir, and doravirine and from 10 to 1800 ng/mL for rilpivirine). This sensitive, accurate, and rapid UHPLC-MS/MS assay is currently applied in our laboratory for routine therapeutic drug monitoring of the oral drugs bictegravir and doravirine and is also intended to be applied for the monitoring of cabotegravir/rilpivirine levels in plasma from PLWH receiving once monthly or every 2-month intramuscular injection of these long-acting antiretroviral drugs.
    Keywords:  UHPLC-MS/MS; antiretroviral therapy; long-acting injectables; pharmacokinetics; therapeutic drug monitoring
    DOI:  https://doi.org/10.1002/jms.4506
  17. Mass Spectrom (Tokyo). 2019 ;8(1): A0078
    Claes BSR, Takeo E, Fukusaki E, Shimma S, Heeren RMA.
      Mass spectrometry imaging is an imaging technology that allows the localization and identification of molecules on (biological) sample surfaces. Obtaining the localization of a compound in tissue is of great value in biological research. Yet, the identification of compounds remains a challenge. Mass spectrometry alone, even with high-mass resolution, cannot always distinguish between the subtle structural differences of isomeric compounds. This review discusses recent advances in mass spectrometry imaging of lipids, steroid hormones, amino acids and proteins that allow imaging with isomeric resolution. These improvements in detailed identification can give new insights into the local biological activity of isomers.
    Keywords:  biological surface; derivatization; instrumentation; isomers; mass spectrometry imaging
    DOI:  https://doi.org/10.5702/massspectrometry.A0078
  18. Anal Methods. 2019 Dec 07. 11(45): 5746-5749
    Rister AL, Bidne KL, Wood JR, Dodds ED.
      Corticosterone is an important steroid for the regulation of metabolism and stress response. Existing methods for the measurement of corticosterone include radioimmunoassay (RIA), enzyme linked immunosorbent assay (ELISA), and liquid chromatography-mass spectrometry (LC-MS). While each of these approaches have their advantages, RIAs use radioactive isotopes that necessitate specially regulated usage and disposal. Furthermore, both ELISAs and RIAs require expensive kits and can only measure a single analyte. In this study, we establish a new sample preparation technique based on a modified Folch extraction that allows for the simultaneous isolation of corticosterone and lipids from serum. The extract is then analyzed by LC-MS. Using only 5 µL of serum, quantification of corticosterone was achieved with coefficients of variation at 3% or less and a detection limit of 0.12 µM. Overall, the results of this study should be beneficial to the measurement of circulating corticosterone and lipids for a variety of studies using small volumes of samples.
    Keywords:  Corticosterone; Lipidomics; Liquid chromatography / mass spectrometry; Steroid quantitation
    DOI:  https://doi.org/10.1039/c9ay01757g
  19. J Chromatogr B Analyt Technol Biomed Life Sci. 2020 Feb 26. pii: S1570-0232(19)31863-X. [Epub ahead of print]1142 122043
    Dang J, Chen C, Ma J, Dawa Y, Wang Q, Tao Y, Wang Q, Ji T.
      Wild edible macro fungi Floccularia luteovirens proved to be a valuable source for the identification of novel lead molecules with therapeutic potential. Nevertheless, the chemical constituents of Floccularia luteovirens are rarely reported due to absence of efficient purification methods. In this study, a hydrophilic interaction chromatography directed by on-line HPLC-DPPH assay has been developed and successfully applied for the isolation of free radical inhibitor from the methanolic extract of Floccularia luteovirens. Using a hydrophilic interaction chromatographic column coupled with the HPLC-DPPH assay for screening the potential radical scavengers, the mid-pressure hydrophilic interaction chromatography (HILIC) proved to be more efficient in the pretreatment stage, yielding the fraction rich in free radical scavengers in good yield (5.9% recovery from 130.0 g of fresh F. luteovirens). From highly potent fraction, the target compound was isolated using the Click XION preparative chromatography with 17.2% recovery. The isolated compound was L-(+)-ergothioneine, where the purity (>95%) and antioxidant activity of were confirmed by chromatography and HPLC-DPPH assay, while the structure of this compound was elucidated from HR ESI-MS and NMR data. This method proved to be very efficient for the recognition and isolation of highly polar free radical inhibitors from fungi extracts, and is also applicable for the purification of highly polar compounds from other sources.
    Keywords:  Floccularia luteovirens; Highly polar free radical inhibitor; Hydrophilic interaction chromatography; On-line HPLC-DPPH assay
    DOI:  https://doi.org/10.1016/j.jchromb.2020.122043
  20. ACS Chem Biol. 2020 Mar 13.
    Flasch M, Bueschl C, Woelflingseder L, Schwartz-Zimmermann HE, Adam G, Schuhmacher R, Marko D, Warth B.
      Xenobiotics are ubiquitous in the environment and modified in the human body by phase I and II metabolism. Liquid chromatography coupled to high resolution mass spectrometry is a powerful tool to investigate these biotransformation products. We present a workflow based on stable isotope-assisted metabolomics and the bioinformatics tool MetExtract II for deciphering xenobiotic metabolites produced by human cells. Its potential was demonstrated by the investigation of the metabolism of deoxynivalenol (DON), an abundant food contaminant, in a liver carcinoma cell line (HepG2) and a model for colon carcinoma (HT29). Detected known metabolites included DON-3-sulfate, DON-10-sulfonate, and DON-10-glutathione as well as DON-cysteine. Conjugation with amino acids and antibiotics was confirmed for the first time. The approach allows the untargeted elucidation of human xenobiotic products in tissue culture. It may be applied to other fields of research including drug metabolism, personalized medicine and systems biology to better understand the relevance of in vitro experiments.
    DOI:  https://doi.org/10.1021/acschembio.9b01016
  21. Anal Sci. 2020 ;36(3): 285-286
    Uchimura T.
      
    Keywords:  Laser abrasion; laser desorption; laser desorption/ionization; matrix-assisted laser desorption ionization; multiphoton ionization
    DOI:  https://doi.org/10.2116/analsci.highlights2003
  22. Analyst. 2020 Mar 12.
    Ouyang D, Luo K, Ma W, Wu J, Li J, He Y, Cai Z, Lin Z.
      A spherical vinyl-functionalized covalent-organic framework (COF-V) was prepared at room temperature by a facile method and applied as a novel substrate for surface-enhanced laser desorption/ionization mass spectrometry (SELDI-MS). Compared with conventional organic matrices, the spherical COF-V with high crystallinity and good monodispersity exhibited high sensitivity, no matrix background interference, wide-range applicability, high salt tolerance and reproducibility in the characterization of small molecules. Considering these advantages, the applicability of the spherical COF-V-based SELDI-MS method was successfully demonstrated by determining trace amounts of glucose in diabetic urine, which would be a promising candidate for clinical diagnosis of diabetes. In addition, the morphological effect and the desorption/ionization mechanism of the COF-V were investigated in detail and the results indicated that the spherical COF-V substrate could greatly enhance the LDI process compared with the bulk COF-V. This work not only extends the application of COFs in MS, but also offers a promising alternative for small molecule identification and clinical diagnosis of diabetes.
    DOI:  https://doi.org/10.1039/d0an00171f
  23. Anal Chem. 2020 Mar 13.
    Smets T, Waelkens E, De Moor B.
      Mass spectrometry imaging (MSI) is a promising technique to assess the spatial distribution of molecules in a tissue sample. Non-linear dimensionality reduction methods such as Uniform Manifold Approximation and Projection (UMAP) can be very valuable for the visualization of the massive datasets produced by MSI. These visualizations can offer us good initial insights regarding the heterogeneity and variety of molecular patterns present in the data, but they do not discern which molecules might be driving these observations. To prioritize the m/z-values associated with these biochemical profiles, we apply a bidirectional dimensionality reduction approach taking into account both the spectral and spatial information. The results show that both sources of information are instrumental to get a more comprehensive view on the relevant m/z-values and can support the reliability of the results obtained using UMAP. We illustrate our approach on heterogeneous pancreas tissues obtained from healthy mice.
    DOI:  https://doi.org/10.1021/acs.analchem.9b05764
  24. Metabolomics. 2020 Mar 07. 16(3): 36
    O'Shea K, Misra BB.
      Metabolomics has evolved as a discipline from a discovery and functional genomics tool, and is now a cornerstone in the era of big data-driven precision medicine. Sample preparation strategies and analytical technologies have seen enormous growth, and keeping pace with data analytics is challenging, to say the least. This review introduces and briefly presents around 100 metabolomics software resources, tools, databases, and other utilities that have surfaced or have improved in 2019. Table 1 provides the computational dependencies of the tools, categorizes the resources based on utility and ease of use, and provides hyperlinks to webpages where the tools can be downloaded or used. This review intends to keep the community of metabolomics researchers up to date with all the software tools, resources, and databases developed in 2019, in one place.
    Keywords:  Annotation; Database; In silico; Metabolite; Metabolomics; Program; Resource; Software; Tool
    DOI:  https://doi.org/10.1007/s11306-020-01657-3
  25. Cancer Res. 2020 Mar 15. 80(6): 1231-1233
    Tan AW, Weljie AM.
      Glioblastoma multiforme (GBM) tumors are highly metabolic and vascularized, yet little has been reported regarding the spatial localization of metabolic activity within these tumors. A mass spectrometry imaging (MSI) study by Randall and colleagues in this issue provides provocative observations of metabolic gradients in xenograft GBM models. The intensity of acylcarnitines is dramatically increased at tumor margins, which interface with normal tissue, but not in tumor margins at the edge of the brain. A secondary examination of drug metabolites suggests that the observed metabolic gradients are pharmacologically relevant. These findings underscore previously undescribed spatial metabolic heterogeneity in GBM biology and opportunities for MSI investigations.See related article by Randall et al., p. 1258.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-0137
  26. Analyst. 2020 Mar 10.
    Giraudeau P.
      NMR spectroscopy is an essential analytical technique in metabolomics and fluxomics workflows, owing to its high structural elucidation capabilities combined with its intrinsic quantitative nature. However, routine NMR "omic" analytical methods suffer from several drawbacks that may have limited their use as a method of choice, in particular when compared to another widely used technique, mass spectrometry. This review describes, in a critical and perspective discussion, how some of the most recent developments emerging from the NMR community could act as real game changers for metabolomics and fluxomics in the near future. Advanced developments to make NMR metabolomics more resolutive, more sensitive and more accessible are described, as well as new approaches to improve the identification of biomarkers. We hope that this review will convince a broad end-user community of the increasing role of NMR in the "omic" world at the beginning of the 2020s.
    DOI:  https://doi.org/10.1039/d0an00142b
  27. J Am Soc Mass Spectrom. 2020 Mar 10.
    Vandergrift GW, Lattanzio-Battle W, Krogh ET, Gill CG.
      Direct mass spectrometry has grown significantly due to wide applicability, relative ease of use, and high sample throughput. However, many current direct mass spectrometry methods are largely based on ambient ionization techniques that can suffer from matrix effects and poor selectivity. A strategy that addresses these shortcomings is condensed phase membrane introduction mass spectrometry-liquid electron ionization utilizing in situ liquid reagent chemical ionization (CP-MIMS-LEI/CI). In CP-MIMS measurements, a semipermeable hollow fiber polydimethylsiloxane membrane probe is directly immersed into a complex sample. Neutral, hydrophobic analytes permeating the membrane are entrained by a continuously flowing liquid acceptor phase (nL/min) to an LEI/CI source, where the liquid is nebulized, followed by analyte vaporization and ionization. This study marks the first intentional exploitation of the liquid CP-MIMS acceptor phase as an in situ means of providing liquid chemical ionization (CI) reagents for improved analyte sensitivity and selectivity (CP-MIMS-LEI/CI). Acetonitrile and diethyl ether were used as a combination acceptor phase/CI proton transfer reagent system for the direct analysis of dialkyl phthalates. Using isotopically labeled reagents, the gas phase ionization mechanism was found to involve reagent autoprotonation, followed by proton transfer to dialkyl phthalates. A demonstration of the applicability of CP-MIMS-LEI/CI for rapid and sensitive screening of bis(2-ethylhexyl) phthalate in house dust samples is presented. The detection limit in house dust (6 mg/kg) is comparable to that obtained by conventional analyses, but without time-consuming sample workup or chromatographic separation steps.
    Keywords:  CP-MIMS-LEI/CI; Liquid reagent chemical ionization; direct mass spectrometry; membrane introduction mass spectrometry; phthalates
    DOI:  https://doi.org/10.1021/jasms.9b00143
  28. Database (Oxford). 2020 Jan 01. pii: baaa011. [Epub ahead of print]2020
    Li D, Ma B, Xu X, Chen G, Li T, He N.
      Mulberry is an important economic crop plant and traditional medicine. It contains a huge array of bioactive metabolites such as flavonoids, amino acids, alkaloids and vitamins. Consequently, mulberry has received increasing attention in recent years. MMHub (version 1.0) is the first open public repository of mass spectra of small chemical compounds (<1000 Da) in mulberry leaves. The database contains 936 electrospray ionization tandem mass spectrometry (ESI-MS2) data and lists the specific distribution of compounds in 91 mulberry resources with two biological duplicates. ESI-MS2 data were obtained under non-standardized and independent experimental conditions. In total, 124 metabolites were identified or tentatively annotated and details of 90 metabolites with associated chemical structures have been deposited in the database. Supporting information such as PubChem compound information, molecular formula and metabolite classification are also provided in the MS2 spectral tag library. The MMHub provides important and comprehensive metabolome data for scientists working with mulberry. This information will be useful for the screening of quality resources and specific metabolites of mulberry. Database URL: https://biodb.swu.edu.cn/mmdb/.
    DOI:  https://doi.org/10.1093/database/baaa011
  29. Expert Opin Drug Discov. 2020 Mar 10. 1-27
    Mohammadi M, Zambare V, Malek L, Gottardo C, Suntres Z, Christopher L.
      Introduction: To date, over 1,000 lichen secondary metabolites have been identified. Despite their promising cytotoxic properties, the number of literature reports on anticancer evaluation of lichenochemicals is limited. As cancer prevalence among the human population increases, there is growing interest in lichens as a natural source of secondary metabolites for anti-cancer drug discovery and development.Areas covered: The lack of significant progress in lichen anticancer research is due to the low levels of cytotoxic compounds contained in lichens, the technical difficulties associated with their isolation and characterization, and the insufficient understanding of their mechanism of action on different cancer cell lines. In this review, the authors discuss these challenges and provide systematically organized information on the limitations and advantages of commonly used and newly developed methods for lichen exploration and screening of lichen secondary metabolites for their anticancer potential.Expert opinion: Recent research activities have demonstrated that lichen secondary metabolites possess chemotherapeutic properties. A systematic and multidisciplinary approach is required to advance lichen research and improve our understanding of the mechanisms responsible for the potent cytotoxic properties of lichenochemicals. More efforts need to focus on screening and discovery of new lichen-derived compounds with unique anticancer properties.
    Keywords:  Anticancer agents; DNA fragmentation; antiproliferation; apoptosis; cancer cell lines; cytotoxicity; extraction; lichenochemicals; lichens; secondary metabolites
    DOI:  https://doi.org/10.1080/17460441.2020.1730325
  30. Mol Inform. 2020 Mar 12.
    Hu J, Cai Y, Li W, Liu G, Tang Y.
      Epoxidation is one of the reactions in drug metabolism. Since epoxide metabolites would bind with proteins or DNA covalently, drugs should avoid epoxidation metabolism in the body. Due to the instability of epoxide, it is difficult to determine epoxidation experimentally. In silico models based on big data and machine learning methods are hence valuable approaches to predict whether a compound would undergo epoxidation. In this study, we collected 884 epoxidation data manually from various sources, and finally got 829 unique sites of epoxidation. Three types of molecular fingerprints with different lengths (1024, 2048 or 4096 bits) were used to describe the reaction sites. Six machine learning methods were used to build the classification models. The training set and test set were randomly divided into 8: 2, and 54 models were constructed and evaluated. Four best models were selected for feature selection. The features were then chosen and verified by external validation set. The resulted optimal model had the accuracy and AUC (area under the curve) values at 0.873 and 0.944 for the test set, 0.838 and 0.987 for the external validation set, respectively. The models built in this study could accurately predict whether a compound will undergo epoxidation and which part is most susceptible to epoxidation, which is of great significance for drug design.
    Keywords:  Machine learning; classification model; epoxidation; site of metabolism
    DOI:  https://doi.org/10.1002/minf.201900178
  31. Bioinformatics. 2020 Mar 13. pii: btaa163. [Epub ahead of print]
    Jiang S, Wang Y, Kaiser M, Krasnogor N.
      MOTIVATION: Flux balance analysis (FBA) based bilevel optimisation has been a great success in redesigning metabolic networks for biochemical overproduction. To date, many computational approaches have been developed to solve the resulting bilevel optimisation problems. However, most of them are of limited use due to biased optimality principle, poor scalability with the size of metabolic networks, potential numeric issues, or low quantity of design solutions in a single run.RESULTS: Here, we have employed a network interdiction (NI) model free of growth optimality assumptions, a special case of bilevel optimisation, for computational strain design and have developed a hybrid Benders algorithm (HBA) that deals with complicating binary variables in the model, thereby achieving high efficiency without numeric issues in search of best design strategies. More importantly, HBA can list solutions that meet users' production requirements during the search, making it possible to obtain numerous design strategies at a small runtime overhead (typically ∼1 hour for examples studied in this paper).
    AVAILABILITY: Source code implemented in the MATALAB Cobratoolbox is freely available at https://github.com/chang88ye/NIHBA.
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaa163
  32. Sci Rep. 2020 Mar 13. 10(1): 4668
    Bhadwal P, Dahiya D, Shinde D, Vaiphei K, Math RGH, Randhawa V, Agnihotri N.
      Perturbations in lipid metabolic pathways to meet the bioenergetic and biosynthetic requirements is a principal characteristic of cancer cells. Sphingolipids (SPLs) are the largest class of bioactive lipids associated to various aspects of tumorigenesis and have been extensively studied in cancer cell lines and experimental models. The clinical relevance of SPLs in human malignancies however is still poorly understood and needs further investigation. In the present study, we adopted a UHPLC-High resolution (orbitrap) Mass spectrometry (HRMS) approach to identify various sphingolipid species in breast cancer patients. A total of 49 SPLs falling into 6 subcategories have been identified. Further, integrating the multivariate analysis with metabolomics enabled us to identify an elevation in the levels of ceramide phosphates and sphingosine phosphates in tumor tissues as compared to adjacent normal tissues. The expression of genes involved in the synthesis of reported metabolites was also determined in local as well as TCGA cohort. A significant upregulation in the expression of CERK and SPHK1 was observed in tumor tissues in local and TCGA cohort. Sphingomyelin levels were found to be high in adjacent normal tissues. Consistent with the above findings, expression of SGMS1 in tumor tissues was downregulated in TCGA cohort only. Clinical correlations of the selected metabolites and their performance as biomarkers was also evaluated. Significant ROC and positive correlation with Ki67 index highlight the diagnostic potential and clinical relevance of ceramide phosphates in breast cancer.
    DOI:  https://doi.org/10.1038/s41598-020-61283-w
  33. Molecules. 2020 Mar 11. pii: E1262. [Epub ahead of print]25(6):
    Biancolillo A, Maggi MA, Bassi S, Marini F, D'Archivio AA.
      Phenoxy acid herbicides are used worldwide and are potential contaminants of drinking water. Reversed phase high-performance liquid chromatography (RP-HPLC) is commonly used to monitor phenoxy acid herbicides in water samples. RP-HPLC retention of phenoxy acids is affected by both mobile phase composition and pH, but the synergic effect of these two factors, which is also dependent on the structure and pKa of solutes, cannot be easily predicted. In this paper, to support the setup of RP-HPLC analysis of phenoxy acids under application of linear mobile phase gradients we modelled the simultaneous effect of the molecular structure and the elution conditions (pH, initial acetonitrile content in the eluent and gradient slope) on the retention of the solutes. In particular, the chromatographic conditions and the molecular descriptors collected on the analyzed compounds were used to estimate the retention factor k by Partial Least Squares (PLS) regression. Eventually, a variable selection approach, Genetic Algorithms, was used to reduce the model complexity and allow an easier interpretation. The PLS model calibrated on the retention data of 15 solutes and successively tested on three external analytes provided satisfying and reliable results.
    Keywords:  HPLC; PLS regression; gradient elution; molecular descriptors; phenoxy acid herbicides; retention prediction
    DOI:  https://doi.org/10.3390/molecules25061262
  34. J Chromatogr A. 2020 Feb 24. pii: S0021-9673(20)30187-4. [Epub ahead of print] 460989
    Heinsvig PJ, Nielsen LS, Lindholst C.
      A GC-MS based analytical method was developed for the profiling of oil-based AAS products using 15 organic constituents as target compounds. A total of 219 compounds were identified in 109 seized AAS products, among them 15 target compounds were selected. The selection was based on each compound's occurrence, reproducibility, and variance between products. The 15 target compounds did not include the active steroid itself, but only compounds found in the carrier oil. The subsequent method validation included assessment of specificity, linearity, precision, robustness and sample stability. The method was finally applied for the classification of a set of 27 seizures of AAS products supplied by the police. The classification was based on the Pearson correlation coefficient using pre-treated peak area data from the 15 target compounds. A successful classification was obtained, with only a small overlap between linked and unlinked samples. A 1% false-positive rate could be obtained at a threshold of 0.625 in terms of the Pearson distance. The present study thus demonstrates that it is possible to profile and classify AAS products with regard to a common origin. As the profiling method is not specific with regards to the steroid content, it may potentially be used to profile and compare other kinds of oil-based liquids.
    Keywords:  Androgenic anabolic steroids (AAS); Drug profiling; Forensic chemistry; Gas chromatography–mass spectrometry (GC–MS)
    DOI:  https://doi.org/10.1016/j.chroma.2020.460989