Discovery of false identification using similarity difference in GC–MS‐based metabolomics

Compound identification is a critical process in metabolomics. The widely used approach for compound identification in gas chromatography–mass spectrometry‐based metabolomics is spectrum matching, in which the mass spectral similarity between an experimental mass spectrum and each mass spectrum in a reference library is calculated. While various similarity measures have been developed to improve the overall accuracy of compound identification, little attention has been paid to reducing the false discovery rate. We, therefore, develop an approach for controlling the false identification rate using the distribution of the difference between the first and second highest spectral similarity scores. We further propose a model‐based approach to achieving a desired true positive rate. The developed method is applied to the National Institute of Standards and Technology mass spectral library, and its performance is compared with that of the conventional approach that uses only the maximum spectral similarity score. The results show that the developed method achieves a significantly higher F1 score and positive predictive value than did the conventional approach. Copyright © 2014 John Wiley & Sons, Ltd.     

Urinary metabolomic study of systemic lupus erythematosus based on gas chromatography/mass spectrometry

Systemic lupus erythematosus (SLE) is an autoimmune disease with heterogeneous organ and system manifestations. In this study, urinary metabolic alterations related to SLE were investigated by performing gas chromatography/mass spectrometry (GC/MS) based metabolomics and multivariate statistical analysis. Patients with SLE and healthy controls could be clearly differentiated in view of the metabolic abnormity in urine. Among 70 identified endogenous metabolites, 23 metabolites were dramatically increased in SLE patients, which involved in several key metabolic pathways including energy metabolism, nucleotide metabolism, oxidative stress and gut‐microbiome‐derived metabolism. This noninvasive and GC/MS‐based metabolomic technique is a promising and potent strategy for identifying novel biomarkers and understanding pathogenesis of SLE. Copyright © 2016 John Wiley & Sons, Ltd.     

Effects of Centella asiatica extract on antioxidant status and liver metabolome of rotenone‐treated rats using GC–MS

Centella asiatica has been used as a culinary vegetable or medicinal herb. In this study, the hepatoprotective effect of the standardized extract of C. asiatica (ECa233) in rotenone‐treated rats was examined using a GC–MS‐based metabolomic approach. ECa233 contains >80% triterpenoids with a ratio of madecassoside to asiaticoside of 1.5(±0.5):1. Rats were randomly divided into three groups (with six rats/group): sham negative control, rotenone positive control and the ECa233 test group. Rats in the ECa233 group received 10 mg/kg ECa233 orally for 20 days, followed by 2.5 mg/kg intraperitoneal rotenone injection to induce toxicity before being sacrificed. Metabolomic analysis showed that supplementation of ECa233 protected rat liver against rotenone toxicity. Pipecolinic acid was one of the most important metabolites; its level was decreased in the rotenone group as compared with the control. Supplementation with ECa233 before administration of rotenone raised pipecolinic acid to levels intermediate between controls and rotenone alone. The metabolomics approach also helped discover a possible new genuine epimetabolite in the present work. Antioxidant tests revealed that ECa233 inhibited lipid peroxidation and increased catalase activities in liver tissue.     

UPLC–QTOF/MS‐based metabolomics reveals the mechanism of chronic unpredictable mild stress‐induced hypertension in rats

Hypertension is a common chronic disease, and it is the strongest risk factor for cardiovascular disease. Recently, the number of patients with hypertension‐related complications has increased significantly, adding a heavy burden to the public health system. It is known that chronic stress plays an important role in the pathogenesis of cardiovascular diseases such as hypertension and stroke. However, the impact of hypertension on the dysfunctions induced by chronic stress remains poorly understood. In this study, using LC–MS‐based metabolomics, we established a chronic stress model to demonstrate the mechanisms of stress‐induced hypertension. We found that 30 metabolites in chronically stressed rats were changed; of these metabolites, seven had been upregulated, and 23 had been downregulated, including amino acids, phospholipids, carnitines and fatty acids, many of which are involved in amino acid metabolism, cell membrane injury, ATP supply and inflammation. These metabolites are engaged in dysregulated pathways and will provide a targeted approach to study the mechanism of stress‐induced hypertension.     

Rapid LC‐MS‐based metabolomics method to study the Fusarium infection of barley

Ultra high performance liquid chromatography with quadrupole/time‐of‐flight mass spectrometry was applied to evaluate the potential of nontarget metabolomic fingerprinting in order to distinguish Fusarium‐infected and control barley samples. First, the sample extraction and instrumental conditions were optimized to obtain the broadest possible representation of polar/medium‐polar compounds occurring in extracts obtained from barley grain samples. Next, metabolomic fingerprints of extracts obtained from nine barley varieties were acquired under ESI conditions in both positive and negative mode. Each variety of barley was tested in two variants: artificially infected by Fusarium culmorum at the beginning of heading and a control group (no infection). In addition, the dynamics of barley infection development was monitored using this approach. The experimental data were statistically evaluated by principal component analysis, hierarchical clustering analysis, and orthogonal partial least‐squares discriminant analysis. The differentiation of barley in response to F. culmorum infection was feasible using this metabolomics‐based method. Analysis in positive mode provided a higher number of molecular features as compared to that performed under negative mode setting. However, the analysis in negative mode permitted the detection of deoxynivalenol and deoxynivalenol‐3‐glucoside considered as resistance‐indicator metabolites in barley.     

基于液相色谱-质谱联用系统的系统性红斑狼疮患者血浆代谢组学分析

应用快速分离液相色谱-串联四极杆飞行时间质谱(RRLC-Q-TOF/MS)系统对系统性红斑狼疮(SLE)患者血浆样本进行代谢指纹图谱的分析。分别应用监督模式识别方法正交信号校正结合偏最小二乘法-判别分析(OSC-PLS-DA)对代谢组数据进行处理,结果显示SLE患者与健康人群对照组的代谢指纹存在明显差异;进一步从SLE患者血清代谢图谱中筛选出10个对分类有显著贡献的离子,定性鉴定出7种代谢标志物,发现SLE患者存在异常的氨基酸、磷脂和卟啉的代谢状态。本研究可为SLE的监测和诊断以及SLE发病的分子基础研究提供科学依据。     

New cathinone‐derived designer drugs 3‐bromomethcathinone and 3‐fluoromethcathinone: studies on their metabolism in rat urine and human liver microsomes using GC–MS and LC–high‐resolution MS and their detectability in urine

3‐Bromomethcathinone (3‐BMC) and 3‐Fluoromethcathinone (3‐FMC) are two new designer drugs, which were seized in Israel during 2009 and had also appeared on the illicit drug market in Germany. These two compounds were sold via the Internet as so‐called “bath salts” or “plant feeders.” The aim of the present study was to identify for the first time the 3‐BMC and 3‐FMC Phase I and II metabolites in rat urine and human liver microsomes using GC–MS and LC–high‐resolution MS (HR‐MS) and to test for their detectability by established urine screening approaches using GC–MS or LC–MS. Furthermore, the human cytochrome‐P450 (CYP) isoenzymes responsible for the main metabolic steps were studied to highlight possible risks of consumption due to drug–drug interaction or genetic variations. For the first aim, rat urine samples were extracted after and without enzymatic cleavage of conjugates. The metabolites were separated and identified by GC–MS and by LC–HR‐MS. The main metabolic steps were N‐demethylation, reduction of the keto group to the corresponding alcohol, hydroxylation of the aromatic system and combinations of these steps. The elemental composition of the metabolites identified by GC–MS could be confirmed by LC–HR‐MS. Furthermore, corresponding Phase II metabolites were identified using the LC–HR‐MS approach. For both compounds, detection in rat urine was possible within the authors' systematic toxicological analysis using both GC–MS and LC–MSⁿ after a suspected recreational users dose. Following CYP enzyme kinetic studies, CYP2B6 was the most relevant enzyme for both the N‐demethylation of 3‐BMC and 3‐FMC after in vitro–in vivo extrapolation. Copyright © 2012 John Wiley & Sons, Ltd.     

Comparison of GC–MS and MEKC methods for caffeine determination in preworkout supplements

In this study, GC–MS‐ and MEKC‐based methods for determination of caffeine (CAF) in preworkout supplements were developed and validated. The proposed protocols utilized minimal sample preparation (simple dilution and syringe filtration). The developed methods achieved satisfactory validation parameters, i.e. good linearity (R² > 0.9988 and R² > 0.9985 for GC–MS‐ and MEKC‐based method, respectively), satisfactory intra‐ and interaccuracy (within 92.6–100.7% for method utilizing GC–MS and 92.1–110.3% for protocol based on MEKC) and precision (CV < 15.9% and CV < 6.3% for GC–MS‐ and MEKC‐based method, respectively) and recovery (within 100.1–100.8% for method utilizing GC–MS and 101.5–106.2% for protocol based on MEKC). The LOD was 0.03 and 3 μg/mL for method utilizing GC–MS and MEKC, respectively. The CAF concentrations determined by GC–MS‐ and MEKC‐based methods were found to be in the range of 8.53–11.23 and 8.20–11.61 μg/mL, respectively. Taking into consideration information on the labels, the investigated supplements were found to contain from 110.0 to 167.3% of the declared CAF content, which confirmed the literature reports on incompatibility of the declared product compositions with real ones. Nevertheless, the consumption of examined supplements as recommended by producers did not lead to exceeding the CAF safe limit of 400 mg per day. Additionally, the MEKC‐based method allowed for detection and identification of vitamin B3 and B6 in all of the investigated supplement samples, which demonstrated that MEKC‐based protocols may be an appropriate assays for simultaneous determination of CAF and vitamins.     

Mechanism Studies of the Conversion of 13C‐Labeled n‐Butane on Zeolite H‐ZSM‐5 by Using 13C Magic Angle Spinning NMR Spectroscopy and GC–MS Analysis

By using ¹³C MAS NMR spectroscopy (MAS=magic angle spinning), the conversion of selectively ¹³C‐labeled n‐butane on zeolite H‐ZSM‐5 at 430–470 K has been demonstrated to proceed through two pathways: 1) scrambling of the selective ¹³C‐label in the n‐butane molecule, and 2) oligomerization–cracking and conjunct polymerization. The latter processes (2) produce isobutane and propane simultaneously with alkyl‐substituted cyclopentenyl cations and condensed aromatic compounds. In situ ¹³C MAS NMR and complementary ex situ GC–MS data provided evidence for a monomolecular mechanism of the ¹³C‐label scrambling, whereas both isobutane and propane are formed through intermolecular pathways. According to ¹³C MAS NMR kinetic measurements, both pathways proceed with nearly the same activation energies (E_a=75 kJ mol^?1 for the scrambling and 71 kJ mol^?1 for isobutane and propane formation). This can be rationalized by considering the intermolecular hydride transfer between a primarily initiated carbenium ion and n‐butane as being the rate‐determining stage of the n‐butane conversion on zeolite H‐ZSM‐5.     

Determination of phthalate esters in bottled water using dispersive liquid–liquid microextraction coupled with GC–MS

Dispersive liquid–liquid microextraction method was developed for the determination of the amount of phthalate esters in bottled drinking water samples and dispersive liquid–liquid microextraction samples were analyzed by GC–MS. Various experimental conditions influencing the extraction were optimized. Under the optimized conditions, very good linearity was observed for all analytes in a range between 0.05 and 150 μg/L with coefficient of determination (R²) between 0.995 and 0.999. The LODs based on S/N = 3 were 0.005–0.22 μg/L. The reproducibility of dispersive liquid–liquid microextraction was evaluated. The RSDs were 1.3–5.2% (n = 3). The concentrations of phthalates were determined in bottled samples available in half shell. To understand the leaching profile of these phthalates from bottled water, bottles were exposed to direct sunlight during summer (temperature from 34–57°C) and sampled at different intervals. Result showed that the proposed dispersive liquid–liquid microextraction is suitable for rapid determination of phthalates in bottled water and di‐n‐butyl, butyl benzyl, and bis‐2‐ethylhexyl phthalate compounds leaching from bottles up to 36 h. Thereafter, degradation of phthalates was observed.     

Analysis of polybrominated diphenyl ethers in sewage sludge by matrix solid‐phase dispersion and isotope dilution GC–MS

A method for the determination of 14 polybrominated diphenyl ethers (PBDEs) in sludge from wastewater treatment plants is presented. PBDEs were extracted by matrix solid‐phase dispersion assisted by sonication and determined by isotope dilution gas chromatography with electron impact mass spectrometric detection in the selected ion monitoring mode, using labelled ¹³C‐PBDEs as internal standards. The limits of detection and quantification for the tri‐ to hepta‐BDEs were in the range of 0.05 to 0.5 ng/g dry weight and 0.15 to 1.8 ng/g dry weight, respectively, and 1.6 ng/g dry weight and 5.6 ng/g dry weight for deca‐BDE‐209. The proposed analytical method was applied to determine PBDE levels in sewage sludge samples collected from 19 water treatment plants located in the province of Madrid (Spain). In all of the examined samples, BDE‐100 and BDE‐154 were the main compounds found with a mean concentration of 3.9 and 2.0 ng/g, respectively. PBDEs were detected in all of the samples, and their total concentrations not considering BDE‐209 were between 3.9 and 23.0 ng/g dry weight. The dominant PBDE congener in sewage sludge was BDE‐209, which constituted 38.7 to 97.3% of the total, and showed concentration levels ranging from 8.1 to 717.2 ng/g dry weight.     

GC–SIM/MS Profiling of Urinary Steroids as their Per-trimethylsilyl Derivatives

Complete GC–SIM/MS separation and identification of 19 steroids (including several steroid isomers) in a male urine sample, as their per-trimethylsilyl ethers, is described. Trimethylsilylation of their functional groups (hydroxyl and carbonyl) was achieved by a rapid, simplified and one-step derivatization method, using N -methyl- N -trimethylsilyl-2,2,2,-trifluoroacetamide as the silylating agent and the solvent as well, along with catalytic amounts of trimethylsilyl iodide and dithioerythritol. Furthermore, a GC/MS method for the analysis of a synthetic mixture of underivatized urinary steroids is proposed. © 1997 by John Wiley & Sons, Ltd.     

High resolution capillary GC–MS analysis of low molecular weight organic compounds in municipal wastewater

High resolution capillary gas chromatography–mass spectrometry has been used in combination with various sample preparation methods to analyze a wide range of low molecular weight organic contaminants in municipal wastewaters. Volatile organic compounds were extracted using a purge and trap concentrator connected directly to a wide bore DB-624 capillary column. Because of the high organic load in wastewater samples, this method was preferred to the more sensitive closed loop stripping technique which suffered from competition effects and insufficient adsorbent capacity. Volatile and semi-volatile base/neutral compounds and acids were extracted with dichloromethane at pH 11 and pH 2, respectively, or were recovered using a simultaneous distillation-extraction procedure. Acidic compounds were subsequently derivatized using diazomethane methylation. Both fractions were separated with a 30m DB-5ms capillary column. Specific ionic substances (LAS, NTA, EDTA) were isolated by solid-phase extraction then derivatized with diazomethane (LAS) or acetyl chloride in n-butanol (NTA, EDTA) before GC–MS analysis. This array of techniques enabled the identification of more than 150 organic contaminants in the influent of a municipal wastewater treatment plant in northern suburban Paris. The individual concentrations of these contaminants ranged from < 0.1 μg/l to 5.7 mg/l.     

Determination of cuticular and internal fatty acids of Chorthippus brunneus males and females using HPLC‐LLSD and GC–MS

Insects are of growing significance in veterinary medicine and human healthcare; therefore, an understanding of their biology is very important. The cuticular and internal fatty acid compositions of Chorthippus brunneus males and females have been studied for the first time. The lipids of males and females were separated into classes of compounds using high‐performance liquid chromatography with a laser light scattering detector. The free fatty acid (FFA) fractions obtained by HPLC were silylated and then analyzed by GC–MS. The cuticular lipids of males contained 15 saturated, four unsaturated with even‐numbered and two unsaturated with odd‐numbered carbon chains, FFAs ranging from C8 to C25. The major free fatty acids in males were C16 (20.8%), C18:2 (8.5%), C18:1 (32.9%) and C18 (24.4%). The cuticular lipids of females contained 17 saturated, four monounsaturated and two diunsaturated free fatty acids ranging from C8 to C30. The major cuticular fatty acids in females were C16 (25.1%), C18:2 (6.2%), C18:1 (23.7%) and C18:0 (33.2%). The internal FFAs of males consisted of 20 compounds ranging from C8 to C26. Four of these compounds were detected as major compounds: C16 (14.1%), C18:2 (21.6%), C18:1 (38.0%) and C18 (22.5%). Among 18 internal free fatty acids of females, C16 (22.3%), C18:2 (10.9%), C18:1 (40.2%) and C18 (20.5%) were the most abundant compounds. The following cuticular fatty acids present in the lipids of females were absent in the lipids of males: C26, C27 and C30. On the other hand, only C24 was absent from the cuticular lipids of females. Only C10 and C24 internal fatty acids present in the lipids of males were absent in the lipids of females. Copyright © 2016 John Wiley & Sons, Ltd.     

Simultaneous quantitation of seven pyrethroid metabolites in human urine by capillary gas chromatography–mass spectrometry

Pyrethroid insecticides are applied in the residential environment, as well as in agricultural crops, for insect control purpose. We developed and validated an accurate, sensitive, and reproducible analytical method to simultaneously detect seven pyrethroid metabolites, namely, 3‐(2,2‐dichlorovinyl)‐2,2‐dimethyl‐(1‐cyclopropane) carboxylic acid, 3‐(2,2‐dibromovinyl)‐2,2‐dimethyl‐(1‐cyclopropane) carboxylic acid, 3‐phenoxybenzoic acid, 4‐fluoro‐3‐phenoxybenzoic acid, 2‐methyl‐3‐phenylbenzoic acid, 4‐chloro‐α‐isoproply benzeneacetic acid, and 3‐(2‐chloro‐3,3,3‐trifluoroprop‐1‐enyl)‐2,2‐dimethylcyclopropanecarboxylic acid, in human urine. This method employs deconjugation with enzyme, SPE using Agilent C18 cartridges on a RapidTrace SPE workstation, derivatization using hexafluoro isopropanol and N,N′‐diisopropylcarbodiimide, and compounds separation and identification on GC–MS. The detection limits of seven metabolites were 0.02–0.08 ng/mL in urine. The recoveries of seven metabolites were 81–104%, 85–99%, and 83–99% in urine specimens fortified at 0.1, 0.4, and 3.2 ng/mL concentrations, respectively. The overall coefficient of variation was 4.3–10.8% in two quality control specimens which were repeatedly measured during a period of 2 months. This method was applied to urine samples collected from children living in Boston, MA. The median concentrations of six detected pyrethroid metabolites ranged from 0.06 to 0.86 ng/mL in urine.     

Simultaneous determination of difenoconazole,trifloxystrobin and its metabolite trifloxystrobin acid residues in watermelon under field conditions by GC–MS/MS

An optimized quick, easy, cheap, effective, rugged and safe method for the simultaneous determination of difenoconazole, trifloxystrobin and its metabolite trifloxystrobin acid residues in watermelon and soil was developed and validated by gas chromatography with tandem mass spectrometry. The samples were extracted with acetonitrile (1% formic acid) and cleaned up by dispersive solid‐phase extraction with octadecylsilane sorbent. The limit of quantification of the method was 0.01 mg/kg, and the limit of detection was 0.003 mg/kg for all three analytes. The recoveries of the fungicides in watermelon, pulp and soil were 72.32–99.20% for difenoconazole, 74.68–87.72% for trifloxystrobin and 78.59–92.66% for trifloxystrobin acid with relative standard deviations of 1.34–14.04%. The dissipation dynamics of difenoconazole and trifloxystrobin in watermelon and soil followed the first‐order kinetics with half‐lives of 3.2–8.8 days in both locations. The final residue levels of difenoconazole and trifloxystrobin were below 0.1 mg/kg (maximum residue level [MRL] set by China) and 0.2 mg/kg (MRL set by European Union), respectively, in pulp samples collected 14 days after the last application. These results could help Chinese authorities to establish MRL of trifloxystrobin in watermelon and provide guidance for the safe and proper application of both fungicides on watermelon.     

Analysis of vaporous contaminants including low‐volatility analytes permeating textiles at room temperature using headspace solid‐phase microextraction GC–MS

Detection of toxic vapors permeating textiles is an important measure of the efficacy of a protective garment. Here, we demonstrate a method to detect and analyze contaminant vapors as they permeate through cotton textiles. Specifically, we show how this method can be improved upon by the incorporation of solid‐phase microextraction into the sampling process, thereby allowing low‐volatility analytes to be sampled at room temperature without significantly influencing the concentration of the contaminant in the headspace. Furthermore, this technique can be extended to other applications in the development of barrier materials as it lends itself to kinetics as well as direct comparison of materials' total chemical permeation. Copyright © 2015 John Wiley & Sons, Ltd.     

GC–MS with photoionization of cold molecules in supersonic molecular beams—Approaching the softest ionization method

A new type of photoionization ion source was developed for the ionization of cold molecules in supersonic molecular beams (named Cold PI). The system was based on a GC–MS with supersonic molecular beams and its fly‐through EI of cold molecules ion source (Cold EI) plus quadrupole mass analyzer. A continuously operated deuterium VUV photoionization lamp was added and placed above and between the supersonic nozzle and skimmer whereas the Cold EI ion source served only as a portion of the ion transfer ion optics. The supersonic nozzle and skimmer were voltage biased and the VUV light crossed the supersonic expansion about 10 mm from the nozzle. We obtained over three orders of magnitude enhancement in the relative abundance of the molecular ion of squalane in Cold PI versus in photoionization of this compound as a thermal compound. Accordingly, we also proved that standard photoionization is not as soft ionization method as previously perceived for large compounds. We found that Cold PI is as soft as and possibly softer than field ionization; thus, it could be the softest known ionization method. The ionization yield was about 200–300 times weaker than with Cold EI yet our limit of detection was about 200 femtogram in SIM mode for cholesterol and pyrene which is reasonable. Practically, all hydrocarbons gave only molecular ions with rather uniform response whereas alcohols gave some molecular ions plus major fragment ions particularly with a loss of water (similarly to field ionization). We tested Cold PI in the GC–MS analysis of diesel fuels and analyzed the time averaged data for group type information. We also found that we can analyze the diesel fuels by fast under 20‐s flow injection analysis in which the generated averaged mass spectrum of molecular ions only could serve for the characterization of fuels.