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.     

Characterization of fluvalinate residues in honey by gas chromatography–atomic emission detection and gas chromatography–mass spectrometry

Two hyphenated techniques, gas chromatography–mass spectrometry and gas chromatography–atomic emission detection, have been used to identify the degradation products of the acaricide fluvalinate in a methanol solution of the commercially available formulation Mavrick, as well as in honey from beehives treated with this product. The major degradation products were 2-chloro-4-trifluoromethylaniline (I), methyl 2-[2-chloro-4-trifluoromethylaniline]-3-methylbutanoate (II), N-(2-chloro-4-trifluoromethyl-phenyl)valine (III), and 3-phenoxybenzaldehyde (IV). Fluvalinate in honey is gradually degraded, 3-phenoxybenzaldehyde being the most abundant residue.     

Application of ultrasound‐assisted liquid–liquid microextraction coupled with gas chromatography and mass spectrometry for the rapid determination of synthetic cannabinoids and metabolites in biological samples

The constant emergence of new psychoactive substances is a challenge to clinical and forensic toxicologists who need to constantly update analytical techniques to detect them. A large portion of these substances are synthetic cannabinoids. The aim of this study was to develop a rapid and simple method for the determination of synthetic cannabinoids and their metabolites in urine and blood using gas chromatography–mass spectrometry. The method involves an ultrasound‐assisted dispersive liquid–liquid microextraction that implies a rapid procedure, giving excellent extraction efficiencies with minimal use of toxic solvents. This is followed by silylation and analysis with gas chromatography–mass spectrometry. The chromatographic method allows for the separation and identification of 29 selected synthetic cannabinoids and some metabolites. The method was validated on urine and blood samples with the ability to detect and quantify all analytes with satisfactory limits of detection (from 1 to 5 ng/mL), limits of quantification (5 ng/mL), and selectivity and linearity (in the range of 5–200 ng/mL). The developed assay is highly applicable to laboratories with limited instrumental availability, due to the use of efficient and low‐cost sample preparation and instrumental equipment. The latter may contribute to enhance the detection of new psychoactive substances in clinical and forensic toxicology laboratories.     

Joint MS‐based platforms for comprehensive comparison of rat plasma and serum metabolic profiling

Metabolomics is a rapidly growing field in the comprehensive understanding of cellular and organism‐specific responses associated with perturbations induced by medicines, chemicals and environment. Blood matrices are frequently used in clinical and biological studies. In this study, we compared metabolic profiling between rat plasma and serum using complementary platforms of gas chromatography–mass spectrometry (GC‐MS) and liquid chromatography–quadruple time‐of‐flight–mass spectrometry (LC‐QTOF‐MS). The sample types that were tested included plasma prepared with K₂EDTA and serum collected using venous blood collection protocols. The results of peak area variation for each detected metabolite/feature in the quality control samples showed a good reproducibility in LC‐QTOF‐MS and better reproducibility in GC‐MS. In GC‐MS analysis: (a) 25.8% of the defined metabolites differed serum from plasma profiling (t‐test, p < 0.05); and (b) serum possessed higher sensitivity than plasma for its generally higher peak intensity in the metabolic profiling. In LC‐QTOF‐MS analysis, 13 (in positive ion mode) and seven (in negative ion mode) important metabolites were identified as mainly contributing to the separation between serum and plasma. Copyright © 2014 John Wiley & Sons, Ltd.     

Simultaneous determination of thirteen kinds of amino acid and eight kinds of acylcarnitine in human serum by LC–MS/MS and its application to measure the serum concentration of lung cancer patients

Easy‐to‐use early cancer detection methods based on metabolomics using serum samples have been developed recently. Among metabolites, amino acids and acylcarnitine are two of the most suitable candidates for diagnosing lung cancer. The purpose of the present study was to develop a novel, sensitive and specific liquid chromatography–tandem mass spectrometry (LC–MS/MS) method to simultaneously determine 13 amino acids and 8 acylcarnitines in lung cancer patients in serum. After derivatization, the 21 analytes were separated using a C₁₈ column with gradient elution program in 14 min, obtaining recovery within 90.4–113.8% and precision within 0.3–14.8%. The method was successfully applied in concentration determination of lung cancer patients and healthy controls. The results showed that the serum concentration of lung cancer patients were significant from those of healthy controls.     

A liquid chromatography–tandem mass spectrometry method to simultaneously determinate dichlorvos and phoxim in tobacco

A simple pretreatment method with liquid chromatography–tandem mass spectrometry (LC–MS/MS) was developed and validated to simultaneously determine dichlorvos and phoxim in tobacco and soil matrices. Satisfactory linearity (R² ≥ 0.9991) of the method was obtained for both analytes. The limits of detection and limits of quantification for dichlorvos and phoxim in three matrices were 0.0015–0.006 and 0.005–0.02 mg/kg, respectively. Average recoveries were 78.24–92.21% for dichlorvos and 76.62–100.51% for phoxim in soil, green tobacco leaves and cured tobacco leaves. The intra‐ and inter‐day relative standard deviations were <6%. The established method was successfully applied for the residual analysis of dichlorvos and phoxim in real soil and tobacco samples. The results indicated that the established method could be used to detect trace amounts of dichlorvos and phoxim in tobacco. The data could also help the Chinese government establish maximum residue limits of dichlorvos and phoxim on tobacco and establish proper and safe use of dichlorvos and phoxim on tobacco plants in China.     

Separation and purification of two minor typical diarrhetic shellfish poisoning toxins from harmful marine microalgae via combined liquid chromatography with mass spectrometric detection

A novel method was developed for the purification of two typical diarrhetic shellfish poisoning toxins from toxin‐producing marine microalgae using macroporous resin, high‐speed countercurrent chromatography–mass spectrometry, and semipreparative high‐performance liquid chromatography–mass spectrometry. Analytical high‐performance liquid chromatography–mass spectrometry was used for identification and purity analysis of okadaic acid and dinophysistoxin‐1 because they exhibit no visible or ultraviolet absorption. First, four kinds of macroporous resins were investigated, and HP‐20 macroporous resin was selected for the preenrichment and cleanup of the two target toxins. Second, the resin‐purified sample was further purified using high‐speed countercurrent chromatography coupled with a mass spectrometer. The purities of the obtained okadaic acid and dinophysistoxin‐1 were 89.0 and 83.0%, respectively, as determined through analytical high‐performance liquid chromatography–mass spectrometry. Finally, further purification was carried out using semipreparative high‐performance liquid chromatography with mass spectrometry, and the purities of the final okadaic acid and dinophysistoxin‐1 products were both over 98.0% based on the analytical high‐performance liquid chromatography–mass spectrometry chromatograms and fraction spectra. This work demonstrates that the proposed purification process is a powerful method for the preparation of high‐purity okadaic acid and dinophysistoxin‐1 from toxin‐producing marine microalgae. Moreover, it is particularly important for the purification and preparation of minor toxins that exhibit no visible or ultraviolet absorption from harmful marine algae.     

Simultaneous determination of residues of thiamethoxam and its metabolite clothianidin in tobacco leaf and soil using liquid chromatography‐tandem mass spectrometry

A simple analytical method was developed to simultaneously determine thiamethoxam and its metabolite, clothianidin, in fresh tobacco leaf, soil and cured tobacco leaf using liquid chromatography with tandem mass spectrometry. Thiamethoxam and clothianidin in tobacco and soil samples were extracted with acetonitrile containing 0.1% formic acid and purified using an NH₂‐SPE column. The optimized method provided good linearity with coefficients of determination R² ≥ 0.9981. The limits of detection and quantification were between 0.006–0.12 and 0.02–0.4 mg/kg, respectively. Intra‐ and inter‐day recovery assays were used to validate the established method. The average recoveries of thiamethoxam and clothianidin in fresh tobacco leaf, soil and cured tobacco leaf were 75.04–100.47%, 75.86–86.40% and 89.83–99.39%, respectively. The intra‐ and inter‐day relative standard deviations were all <9%. The developed method was successfully applied for the analysis of thiamethoxam and clothianidin residues in actual tobacco and soil samples. The results indicated that the established method met the requirements for the analysis of trace amounts of thiamethoxam and clothianidin in fresh tobacco leaf, soil and cured tobacco leaf.     

Screening for inherited metabolic diseases using gas chromatography–tandem mass spectrometry (GC–MS/MS) in Sichuan,China

The aim of this study was to retrospectively diagnose and confirm inherited metabolic diseases (IMD), from a small population of IMD high‐risk patients, with the aid of gas chromatography–tandem mass spectrometry (GC–MS/MS), technologies yet to be popularized in Sichuan, China. Using GC–MS/MS coupled with clinical diagnosis, we retrospectively analyzed samples of dried blood spots and urine specimen from 183 IMD high‐risk infant patients, who visited the West China Second Hospital of Sichuan University between June 2013 and October 2015. Four out of 183 IMD high‐risk infant patients were finally diagnosed to be IMD positive, among which two patients were identified with phenylketonuria, one with maple syrup urine disease, and 1 with methylmalonic academia. Restrictive diets and other symptomatic treatments were employed to treat the confirmed infant patients whose conditions are still under tracking and there are zero cases of death so far. GC–MS/MS was found to be an efficient and reliable way to detect IMD. It is necessary to apply GC–MS/MS, in addition to other clinical approaches, for diagnosing candidate IMD patients so that the confirmed patients can get medical intervention and timely treatment.     

Recent Progress in Mass Spectrometry-based Metabolomics for Colorectal Cancer

Metabolomics, one of the latest omics technologies, is employed to reveal overall metabolic trajectories, identify disease causative mechanisms and provide information for preventive diagnosis and drug targeting. Cancer is a disease known to alter cellular metabolism and so metabolomics can play an important role in the early diagnosis of cancer and in the evaluation of medical interventions and treatments for cancer. Many metabolomics studies rely on high-sensitive and high-throughput mass spectrometry platforms. In recent years, various mass spectrometry(MS) methodologies have been developed and enriched the scope of metabolite detection, contributing to disease studies, such as diabetes, cancer, and depression. Colorectal cancer is the third most diagnosed cancer worldwide and its incidence ranked third in China. This review focuses on the mass spectrometry technologies in metabolomics and summarizes the progress of metabolomics research in colorectal cancer.     

Development and validation of a liquid chromatography–tandem mass spectrometry method for topotecan determination in beagle dog plasma and its application in a bioequivalence study

Topotecan (TPT) is an important anti‐cancer drug that inhibits topoisomerase I. A sensitive and robust liquid chromatography–tandem mass spectrometry (LC‐MS/MS) method that potentially determines TPT in beagle dog plasma is needed for a bioequivalence study of TPT formulations. We developed and validated LC‐MS/MS to evaluate TPT in beagle dog plasma in terms of specificity, linearity, precision, accuracy, stability, extraction recovery and matrix effect. Plasma samples were treated with an Ostro^TM sorbent plate (a robust and effective tool) to eliminate phospholipids and proteins before analysis. TPT and camptothecin (internal standard) were separated on an Acquity UPLC BEH C₁₈ column (1.7 µm, 2.1 × 50 mm) with 0.1% formic acid and methanol as the mobile phase at a flow rate of 0.25 mL/min. TPT was analyzed using positive ion electrospray ionization in multiple‐reaction monitoring mode. The obtained lower limit of quantitation was 1 ng/mL (signal‐to‐noise ratio > 10). The standard calibration curve for TPT was linear (correlation coefficient > 0.99) at the concentration range of 1–400 ng/mL. The intra‐day and inter‐day precision, accuracy, stability, extraction recovery and matrix effect of TPT were within the acceptable limits. The validated method was successfully applied in a bioequivalence study of TPT in healthy beagle dogs. Copyright © 2013 John Wiley & Sons, Ltd.     

Gas Chromatographic–Mass Spectrometric Analysis of Hydrocarbons and Other Neutral Organic Compounds in Volcanic Gases Using SPME for Sample Preparation

Knowledge of the chemical composition of volcanic exhalation is important in providing information on volcanic feeding systems and on the characteristics of the gaseous compounds emitted into the atmosphere. This paper reports a novel analytical method that makes use of capillary gas chromatography coupled to mass spectrometry, preceded by solid-phase micro extraction for sample enrichment. Such an approach enables considerable expansion of the number of neutral organic compounds that can be positively identified in volcanic exhalation. Data obtained from analysis of real samples are also reported.     

Analytical procedures for quantification of peptides in pharmaceutical research by liquid chromatography–mass spectrometry

Peptide quantification by liquid chromatography–mass spectrometry (LC–MS) combines the high resolving power of reversed-phase (RP) chromatography with the excellent selectivity and sensitivity of mass spectrometric detection. On the basis of comprehensive practical experience in the analysis of small molecules, pharmaceutical research is developing technologies for analysis of a growing number of peptidic drug candidates. This article is a detailed review of procedures based on LC–MS techniques for quantitative determination of peptides. With the focus on pharmaceutical applications several technologies for sample preparation, various aspects of peptide chromatography, important characteristics of ESI–MS, selectivity of MS-detection modes, the large variability of internal standards, and modern instrumentation are discussed. The demand for reliable, robust, sensitive, and accurate methods is discussed using numerous examples from the literature, complemented by experiments and results from our laboratory.     

Surrogate analyte‐based quantification of main endocannabinoids in whole blood using liquid chromatography–tandem mass spectrometry

Endocannabinoids (eCBs) are endogenous ligands of the endocannabinoid system that are known to regulate several physiological and behavioral processes. Previous studies have developed methods for the detection of main eCBs including arachidonylethanolamide (AEA) and 2‐arachidonoylglycerol (2‐AG), mostly in serum or plasma. Whole blood is a superior biomaterial for eCBs analysis owing to the nature of the shortened isolation procedure and decreased risk of 2‐AG isomerization during preparation. In this study, a surrogate analyte‐based liquid chromatography–tandem mass spectrometry assay was developed for the measurement of AEA, 2‐AG and its isomer 1‐arachidonoylglycerol (1‐AG) using a maximum of 100 μL whole blood. Chromatographic separation was achieved using a reverse‐phase column and a gradient elution. Detection was performed in selected reaction monitoring mode with an electrospray ionization source. The limits of detection of three eCBs were 0.05–0.1 ng/mL. Good linearity was observed over the concentration range. Intra‐ and inter‐assay accuracy and precision were ≤10.9 and ≤8.7% at four quality control levels. The response factor and parallelism experiment illustrated that the surrogate analytes were suitable for accurate quantification of the main eCBs in whole blood. This surrogate analyte approach was successfully applied to authentic blood samples obtained from alcohol negative drivers and those under the influence of alcohol.     

Development of simultaneous analysis of tryptophan metabolites in serum and gastric juice – an investigation towards establishing a biomarker test for gastric cancer diagnosis

To evaluate changes in tryptophan metabolism and discover diagnostic biomarkers for gastric cancer, a quantitative method was developed for tryptophan and its seven metabolites (indole‐3‐lactic acid, anthranilic acid, serotonin, nicotinic acid, kynurenic acid, kynurenine and 3‐indoxyl sulfate) in both human serum and gastric juice using liquid chromatography–tandem mass spectrometry (LC–MS/MS). Serum and gastric juice were prepared with a simple protein precipitation using aqueous 0.1% formic acid and acetonitrile. As a result, it was found that the kynurenine pathway of tryptophan metabolism was activated in gastric cancer and that the metabolic ratio of kynurenine/tryptophan, which reflects the enzyme activity of indoleamine‐2,3‐dioxygenase, was associated with the observed metabolic changes. Finally, the investigation of tryptophan metabolites, especially kynurenic acid, in serum and gastric juice might serve as biomarkers for gastric cancer. The findings in this study provide critical information of tryptophan metabolism which can be applied to a serum‐based diagnostic test for gastric cancer.     

Accelerated,untargeted metabolomics analysis of cutaneous T‐cell lymphoma reveals metabolic shifts in plasma and tumor adjacent skins of xenograft mice

Cutaneous T‐cell lymphoma (CTCL) is a heterogeneous group of skin‐homing T‐cell neoplasms. Clinical management is stage based but diagnosis and prognosis could be extremely challenging. The presented study aims to explore the metabolic profiling of CTCL by an accelerated untargeted metabolomics data analysis tool “Mummichog” to facilitate the discoveries of potential biomarkers for clinical early stage diagnosis, prognosis, and treatments in CTCL. Ultra high‐performance liquid chromatography–quadrupole time‐of‐flight–based untargeted metabolomics were conducted on the skin and plasma of CTCL mice. It showed that the metabolism of skin changed greatly versus control samples in the development of CTCL. Increased l ‐glutamate and decreased adenosine monophosphate were the most essential metabolic features of CTCL tumor and tumor adjacent skins. Unique metabolism changes in tumor adjacent non‐involved skin tissues (ANIT) occurred in the progress of carcinogenesis, including upregulated cytidine‐5′‐triphosphate, aberrant biosynthesis of prostaglandins, pyrimidine, mevalonate pathway, and tryptophan degradation. Sharply elevated 5‐phospho‐α‐d ‐ribose 1‐diphosphate (PRPP) marked the final state of tumor in CTCL. In the plasma, systematic shifts in corticosterone, sphingolipid, and ceramide metabolism were found. These uncovered aberrant metabolites and metabolic pathways suggested that the metabolic reprogramming of PRPP in tumor tissues may cause the disturbance of cytidine and uridine metabolic homeostasis in ANIT. Accumulative cytidine‐5′‐triphosphate in ANIT may exert positive feedback on the PRPP level and leads to CTCL further development. In addition, the accelerated data analysis tool “Mummichog” showed good practicability and can be widely used in high‐resolution liquid chromatography mass spectrometry–based untargeted metabolomics.     

Bioanalytical technique for determination of tasimelteon in human plasma by LC–MS/MS and its application to pharmacokinetic study in humans

A highly sensitive, specific and rapid liquid chromatography–tandem mass spectrometry technique for the quantification of tasimelteon in human plasma has been developed and validated using tasimelteon‐d₅ as internal standard. Liquid–liquid extraction technique with ethyl acetate was used for extraction of tasimelteon from the plasma. The chromatographic separation was achieved on an Agilent Zorbax, Eclipse, C₁₈ (4.6 × 50 mm, 5 μm) column using a mobile phase of acetonitrile and 0.02% formic acid buffer (85:15, v/v) with a flow rate of 0.5 mL/min. A detailed method validation was performed as per the United States Food and Drug Administration guidelines. The linear calibration curve was obtained over the concentration range 0.30–299 ng/mL. The API‐4000 liquid chromatography–tandem mass spectrometry was operated under multiple reaction monitoring mode during analysis. The validated method was successfully applied to estimate plasma concentration of tasimelteon after oral administration of a single dose of a 20 mg capsule in healthy volunteers under fasting conditions. The maximum concentration of the drug achieved in the plasma was 314 ± 147 ng/mL and the time at which this concentration was attained was 0.54 ± 0.22 h.     

Analysis of Polyunsaturated Fatty Acids Using High Performance Liquid Chromatography – Atmospheric Pressure Chemical Ionization Mass Spectrometry

Analysis of polyunsaturated fatty acids using high performance liquid chromatography–atmospheric pressure chemical ionization mass spectrometry is described. The standard fatty acid methyl esters from 16 to 22 carbons were analyzed by LC‐MS with APCI. The effect of orifice voltage and total carbon atoms versus number of double bonds in each homologue on the mass spectra is discussed. The correction coefficients for homologues from saturated fatty acids to hexaenoic acid are also mentioned.     

Detection of β-blocking drugs in urine by capillary column gas chromatography-negative ion chemical ionization mass spectrometry

β-Blocking drugs present in commercial pharmaceutical products are determined in present urine of volunteers between 4 and 24 hours after the administration of a therapeutical dose. The drugs are extracted, hydrolysed, derivatized with pentafluoropropionic anhydride, and analyzed by capillary gas chromatography and electron capture detection. Metabolite identification and drug confirmation is by capillary gas chromatography–negative ion chemical ionization mass spectrometry (GC-NICIMS). This method is very specific and a sensitivity below 1 ng/ml is obtained.     

Identification of intact oxidation products of glycerophospholipids in vitro and in vivo using negative ion electrospray iontrap mass spectrometry

Free radical‐induced oxidation products of polyunsaturated fatty acids esterified to phospholipids have been implicated in a number of human diseases including atherosclerosis and neurodegenerative diseases. Some of these phospholipid oxidation products have potent biological activities and likely contribute to human pathophysiological conditions. Oxidation products have also been used as markers of oxidative stress in vivo. Identification and quantification of phospholipid oxidation products are often performed by analyzing the oxidized free fatty acid moieties after hydrolysis from the phospholipids head groups by gas chromatography–mass spectrometry (GC–MS) or liquid chromatography–mass spectrometry (LC–MS). We now describe the definitive identification of intact oxidized products of glycerophospholipids including glycerophosphatidylcholine (GPC), glycerophosphatidylethanolamine (GPE), and glycerophosphatidylserine (GPS) in vitro and in vivo using iontrap MS. For these analyses, the negative ions of the oxidation products of phospholipids are fragmented to MSⁿ and unequivocal structural characterization is obtained based on collision‐induced dissociation (CID) of the sn‐2 carboxylate ion. This technique overcomes the need to hydrolyze fatty acids from phospholipids in the analysis. The method has been used to identify a number of oxidation products of glycerophospholipids including hydroxyeicosatetraenoates (HETEs) and isoprostanes (IsoPs) esterified to different classes of glycerophospholipids in vitro and in vivo. These studies thus provide a new approach to identify the intact oxidation products of glycerolphospholipids. Copyright © 2009 John Wiley & Sons, Ltd.