Development of a metabolomic approach based on urine samples and direct infusion mass spectrometry

The analysis of urine by direct infusion mass spectrometry suffers from ion suppression due to its high salt content and inter-sample variability caused by the differences in urine volume between persons. Thus, urine metabolomics requires a careful selection of the sample preparation procedure and a normalization strategy to deal with these problems. Several approaches were tested for metabolomic analysis of urine samples by direct infusion electrospray mass spectrometry (DI–ESI–MS), including solid phase extraction, liquid–liquid extraction, and sample dilution. In addition, normalization of results based on conductivity values and statistical treatment was performed to minimize sample variability. Both urine dilution and solid phase extraction with mixed mode sorbent considerably reduced the salt content in urine, providing comprehensive metabolomic fingerprints. Moreover, statistical data normalization enabled the correction of inter-sample physiological variability, improving the quality of results obtained. Therefore, high-throughput DI–ESI–MS fingerprinting of urine samples can be achieved with simple pretreatment procedures allowing the use of this noninvasive sampling in metabolomics. Finally, the optimized approach was tested in a pilot metabolomic investigation of urine samples from transgenic mice models of Alzheimer’s disease (APP/PS1) in order to illustrate the potential of the methodology.     

Solvent and solid-phase extraction of natural and synthetic anabolic steroids in human urine

Liquid–liquid (using dichloromethane) and liquid–solid extraction processes (using disposable C₁₈ cartridges) were applied to human urine samples spiked with 15 androgenic anabolic steroids (natural and synthetic). The extraction recoveries were assessed from different HPLC separations of anabolic steroids using water–acetonitrile mobile phase, and using calibration graphs obtained by injection into HPLC of standard samples of these compounds before and after extraction. The procedures, including sample preconcentration, showed extraction efficiencies over 90% which were independent on a wide range of concentrations tested. Solid phase extraction yielded poor results for oximetolone, danazol and dehydroepiandrosterone. For real urine samples, hydrolysis using β-glucuronidase and washing using sodium hydroxide before and after solvent extraction, respectively, is recommended.     

Long-Term Frozen Storage of Urine Samples: A Trouble to Get PCR Results in Schistosoma spp. DNA Detection?

Background

Human schistosomiasis remains a serious worldwide public health problem. At present, a sensitive and specific assay for routine diagnosis of schistosome infection is not yet available. The potential for detecting schistosome-derived DNA by PCR-based methods in human clinical samples is currently being investigated as a diagnostic tool with potential application in routine schistosomiasis diagnosis. Collection of diagnostic samples such as stool or blood is usually difficult in some populations. However, urine is a biological sample that can be collected in a non-invasive method, easy to get from people of all ages and easy in management, but as a sample for PCR diagnosis is still not widely used. This could be due to the high variability in the reported efficiency of detection as a result of the high variation in urine samples’ storage or conditions for handling and DNA preservation and extraction methods.

Methodology/Principal Findings

We evaluate different commercial DNA extraction methods from a series of long-term frozen storage human urine samples from patients with parasitological confirmed schistosomiasis in order to assess the PCR effectiveness for Schistosoma spp. detection. Patientś urine samples were frozen for 18 months up to 7 years until use. Results were compared with those obtained in PCR assays using fresh healthy human urine artificially contaminated with Schistosoma mansoni DNA and urine samples from mice experimentally infected with S. mansoni cercariae stored frozen for at least 12 months before use. PCR results in fresh human artificial urine samples using different DNA based extraction methods were much more effective than those obtained when long-term frozen human urine samples were used as the source of DNA template.

Conclusions/Significance

Long-term frozen human urine samples are probably not a good source for DNA extraction for use as a template in PCR detection of Schistosoma spp., regardless of the DNA method of extraction used.     

Spatial and temporal variation in malaria transmission in a low endemicity area in northern Tanzania

Background

Current detection or screening for malaria infection necessitates drawing blood by fingerprick or venipuncture, which poses risks and limitations for repeated measurement. This study presents PCR detection of Plasmodium falciparum in human urine and saliva samples, and illustrates this potential application in genotyping malaria infections.

Methods

Urine and saliva were obtained from 47 thick film positive and 4 negative individuals one day after collection of blood slides and filter paper blood spots. P. falciparum DNA was extracted from blood, urine and saliva, in separate groups, using the Chelex method or Qiagen DNEasy^® kit (urine and saliva only). Blood, urine and saliva extracts were subjected to PCR in separate batches. Amplicons from the various sample types were examined for MSP2 polymorphisms and restriction fragment patterns on DHFR amino acid codon 59.

Results and discussion

Malaria infections exhibited primarily low-grade parasite densities, with a geometric mean of 775 asexual parasites/μl. Regularly matching polymorphic MSP2 genotypes were found between the corresponding urine, saliva and peripheral blood amplicons of each individual, with different inter-individual polymorphic genotypes. Amplicon yields were significantly dependent on DNA extraction method, parasite density and primer set (p < 0.001). A Qiagen^® kit extraction had more than 2× higher amplicon yield than the Chelex method, for both urine and saliva. Amplicon yields were 1.6 fold higher from saliva than urine. For each unit increase in log parasite density, the probability of amplicon enhanced 1.8 fold. Highest amplicon yields were obtained from the primer set with the shortest PCR product.

Conclusion

P. falciparum infection is detectable by PCR on human urine and saliva samples. Subject to further refinement of extraction technique and amplicon yields, large-scale malaria parasite screening and epidemiological surveys could be possible without the need to collect blood and use of needles or sharps.     

Simple and sensitive high-performance liquid chromatographic method for the determination of 1,5-benzodiazepine clobazam and its active metabolite N-desmethylclobazam in human serum and urine with application to 1,4-benzodiazepines analysis

A HPLC–UV determination of clobazam and N-desmethylclobazam in human serum and urine is presented. After simple liquid–liquid extraction with dichloromethane the compounds and an internal standard diazepam were separated on a Supelcosil LC-8-DB column at ambient temperature under isocratic conditions using the mobile phase: CH₃CN–water–0.5 M KH₂PO₄–H₃PO₄ (440:540:20:0.4, v/v and 360:580:60:0.4, v/v for serum and urine, respectively). The detection was performed at 228 nm with limits of quantification of 2 ng/ml for serum and 1 ng/ml for urine. Relative standard deviations for intra- and inter-assay precision were found below 8% for both compounds for all the tested concentrations. The described procedure may be easily adapted for several 1,4-benzodiazepines.     

Stereoselective determination of R,S-2-[4-(3-methyl-2-thienyl)phenyl]propionic acid and its taurine conjugates in dog urine by high-performance liquid chromatography

Two high-performance liquid chromatographic methods for the stereoselective determination of R,S-2-[4-(3-methyl-2-thienyl)-phenyl]propionic acid (R,S-MTPPA), a new anti-inflammatory agent, and its taurine conjugates (R,S-MTPPA-TAU) in dog urine have been developed and validated. The urine samples were subjected to solid extraction or TLC preparation, then R,S-MTPPA and R,S-MTPPA-TAU were separated on Chiralcel OD and Chiral AGP columns, respectively, with ultraviolet absorbance detection at 272 nm. The dose–response relationships for enantiomers of R,S-MTPPA and R,S-MTPPA-TAU were linear in the concentration ranges of 0.5–50 (r>0.9993) and 5–200 μg/ml (r>0.9982), respectively. Recoveries of all tested enantiomers from dog urine were roughly 90% within the above concentration ranges. Intra- and inter-day reproducibilities were sufficient for metabolic studies. These methods were applied to stereoselective determination of the enantiomers in dog urine after administration of either S- or R-MTPPA.     

Evaluation of the Siemens VERSANT® CT/GC DNA 1.0 assay (kPCR) for detection of Chlamydia trachomatis and Neisseria gonorrhoeae

The Siemens VERSANT kPCR system is an automated system which combines extraction of nucleic acids from 96 samples with subsequent real-time PCR. The VERSANT CT/GC DNA 1.0 (kPCR) assay detects Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) in a multiplex real-time PCR on this system. We compared this assay with the BD ProbeTe™ ET System (PT) and the Roche Cobas Amplicor (CA). Three different sets of samples were tested in the kPCR: PT pre-treated samples, prospectively collected urine samples during routine CT/GC testing and urine samples obtained in a blinded fashion by an external lab facility. Agreement of kPCR with the comparator tests was > 0.99 for sample set I and complete agreement was observed for sample set II and III. The kPCR assay demonstrated to be an easy to use robust diagnostic platform. A few modifications to the manufacturer's instructions are recommended to intercept false positivity. We advise to retest samples with Cq values above 35 cycles at least one time and we suggest checking the amplification curves.     

Determination of the antihypertensive drug cilazapril and its active metabolite cilazaprilat in pharmaceuticals and urine by solid-phase extraction and high-performance liquid chromatography with photometric detection

A liquid chromatographic method with photometric detection for the determination of cilazapril and its active metabolite and degradation product cilazaprilat in urine and pharmaceuticals has been developed. The chromatographic method consisted of a μBondapak C₁₈ column maintained at 30±0.2°C, using a mixture of methanol-10 mM phosphoric acid (50:50 v/v) as mobile phase at a flow-rate of 1.0 ml/min. Enalapril maleate was used as internal standard. The detection was performed at a wavelength of 206 nm. A study of the retention of cilazapril and cilazaprilat using solid–liquid extraction has been carried out in order to optimise the clean-up procedure for urine samples, which consisted of a solid–liquid extraction using C₈ cartridges. Recoveries greater than 85% are obtained for both compounds. The method was sensitive, precise and accurate enough to be applied to the determination of urine samples obtained from three hypertensive patients up to 24 h after intake of a therapeutic dose (detection limit of 70 ng/ml for cilazapril and cilazaprilat in urine). A comparison of the method developed using photometric and amperometric detection has been carried out.     

The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis

Background

Urogenital schistosomiasis due to Schistosoma haematobium is a serious underestimated public health problem affecting 112 million people - particularly in sub-Saharan Africa. Microscopic examination of urine samples to detect parasite eggs still remains as definitive diagnosis. This work was focussed on developing a novel loop-mediated isothermal amplification (LAMP) assay for detection of S. haematobium DNA in human urine samples as a high-throughput, simple, accurate and affordable diagnostic tool to use in diagnosis of urogenital schistosomiasis.

Methodology/Principal Findings

A LAMP assay targeting a species specific sequence of S. haematobium ribosomal intergenic spacer was designed. The effectiveness of our LAMP was assessed in a number of patients´ urine samples with microscopy confirmed S. haematobium infection. For potentially large-scale application in field conditions, different DNA extraction methods, including a commercial kit, a modified NaOH extraction method and a rapid heating method were tested using small volumes of urine fractions (whole urine, supernatants and pellets). The heating of pellets from clinical samples was the most efficient method to obtain good-quality DNA detectable by LAMP. The detection limit of our LAMP was 1 fg/µL of S. haematobium DNA in urine samples. When testing all patients´ urine samples included in our study, diagnostic parameters for sensitivity and specificity were calculated for LAMP assay, 100% sensitivity (95% CI: 81.32%-100%) and 86.67% specificity (95% CI: 75.40%-94.05%), and also for microscopy detection of eggs in urine samples, 69.23% sensitivity (95% CI: 48.21% -85.63%) and 100% specificity (95% CI: 93.08%-100%).

Conclusions/Significance

We have developed and evaluated, for the first time, a LAMP assay for detection of S. haematobium DNA in heated pellets from patients´ urine samples using no complicated requirement procedure for DNA extraction. The procedure has been named the Rapid-Heat LAMPellet method and has the potential to be developed further as a field diagnostic tool for use in urogenital schistosomiasis-endemic areas.     

Determination of piromidic acid residues in trout muscle tissue and in urine by liquid chromatography with post-column modification of pH and fluorimetric detection

A rapid high-performance liquid chromatographic method has been developed to determine piromidic acid in trout muscle tissue and in urine, in the presence of nalidixic, 7-hydroxymethylnalidixic, oxolinic and pipemidic acids and cinoxacin. A Nova-Pak C₁₈ column was used with acetonitrile–4·10⁻⁴ M oxalic acid (40:60, v/v) as the mobile phase. A post-column change of pH was made with NaOH. Fluorimetric detection at 456 nm (λ_ex 275 nm) was used. The instrumental detection limit was 5.91 ng/ml, based on height of peak. Pretreatment of the urine samples was not necessary and fish samples were extracted with sodium hydroxide solutions and cleaned by means of an extraction with chloroform. Detection limit was 147 ng/ml for urine and 5.91 ng/g for trout muscle. Good separation without interference from any other components was obtained. Recovery was better than 87% in urine and better than 72% in trout muscle tissue.     

Determination of amoxicillin in body fluids by reversed-phase liquid chromatography coupled with a post-column derivatization procedure

Quantitative methods for determination of amoxicillin in body fluids are described. They comprise separation by reversed-phase chromatography (LiChrosorb RP-8, 5 μm) of the aqueous supernatants obtained from plasma or urine after purification steps involving protein precipitation followed by extraction in the case of plasma, or a double extraction procedure in the case of urine, post-column derivatization with air segmentation, and finally measurement of the UV absorbance at 310 nm. The derivatization involves formation of the mercuric mercaptide of penicillenic acid and is specific for compounds with an intact penicillanic acid ring system.Detection limits achieved on injecting 200 μl of plasma and 20 μl of urine are about 25 ng/ml and 200 ng/ml, respectively, but it is possible to improve the sensitivity further by injecting larger volumes. Precisions (s_rel) obtained for determination of 0.10 and 0.45 μg/ml in plasma were 3.72 and 1.40%, respectively.Some problems regarding column stability originating from the injection of biological samples are discussed.     

Application of solid-phase microextraction and gas chromatography–mass spectrometry for the determination of chlorophenols in urine

This study investigated the feasibility of applying solid-phase microextraction (SPME) combined with gas chromatography–mass spectrometry to analyze chlorophenols in urine. The SPME experimental procedures to extract chlorophenols in urine were optimized with a polar polyacrylate coated fiber at pH 1, extraction time for 50 min and desorption in GC injector at 290°C for 2 min. The linearity was obtained with a precision below 10% R.S.D. for the studied chlorophenols in a wide range from 0.1 to 100 μg/l. In addition, sample extraction by SPME was used to estimate the detection limits of chlorophenols in urine, with selected ion monitoring of GC–MS operated in the electron impact mode and negative chemical ionization mode. Detection limits were obtained at the low ng/l levels. The application of the methods to the determination of chlorophenols in real samples was tested by analyzing urine samples of sawmill workers. The chlorophenols were found in workers, the urinary concentration ranging from 0.02 μg/l (PCP) to 1.56 μg/l (2,4-DCP) depending on chlorophenols. The results show that trace chlorophenols have been detected with SPME–GC–MS in the workers of sawmill where chlorophenol-containing anti-stain agents had been previously used.     

Extraction and purification of tRNA from fruit tissues

Readily measurable yields of undamaged tRNA were obtained from tomato, pear and apple fruits by phenolic extraction at pH 8.8, removal of interfering alcohol insoluble substances by precipitation with 0·2 volumes of iso-PrOH and final purification by DEAE chromatography. Various other commonly used extraction and purification procedures were tested and found to be less effective. Active synthetases were isolated from acidic fruit tissues by adequate control of pH and maceration in the frozen state. After acylation with a radioactively labelled amino acid, fruit isoacceptor tRNA species were separated by reverse phase chromatography.     

Chromatographic analysis of griseofulvin and metabolites in biological fluids

A simple and accurate assay for the determination of griseofulvin and its metabolites in biological fluids using high-performance liquid chromatography is described. Using a reversed phase column and a mobile phase solvent of 45% acetonitrile in 0.1 M acetic acid, baseline separation of griseofulvin and several analogues was obtained. The described method allows one to quantitatively determine griseofulvin, 6-demethylgriseofulvin, and griseofulvic acid, a newly identified metabolite in man, in urine and plasma samples. Treatment of plasma samples prior to the analysis is simply made by deproteinizing the samples with an equal volume of acetonitrile. For urine samples, the procedure involves diethyl ether extraction with subsequent evaporation to dryness and reconstitution with the mobile phase solvent.     

Determination of some benzodiazepines and metabolites in serum,urine and saliva by high-performance liquid chromatography

The performance of a number of liquid—solid systems, consisting of mixtures of buffers (0.05 M) and methanol as mobile phase and methyl-silica as stationary phase, were investigated with respect to their use in the separation of 1,4-benzodiazepines by reversed-phase high-performance liquid chromatography with UV detection at 254 nm. Phase system selectivities and column efficiencies were determined. A nomogram is presented from which the chromatographic parameters can be calculated.A complete separation of nine benzodiazepines within 12 min has been achieved, using methyl-silica as the stationary phase and 50% methanol as the eluent.The results were applied to the development of a method for the determination of therapeutic levels of diazepam and its metabolites in human serum, urine and saliva. The first step in the analysis, the extraction of diazepam and its metabolites from serum and urine, was also investigated and good recoveries were achieved. A low detection limit (0.2 ng) and high precision were obtained. The concentrations of diazepam and its metabolites in human serum, urine and saliva were determined after both single and multiple oral doses of diazepam (and oxazepam).     

核桃楸叶片中总黄酮的最佳提取工艺研究

利用超声波法对核桃楸叶片中总黄酮的提取工艺进行了研究,在单因素试验的基础上,采用正交试验法,确立最佳提取条件,考察乙醇浓度、提取温度、液料比和提取时间对核桃楸叶片总黄酮提取率的影响。结果表明：超声波法辅助提取核桃楸叶片总黄酮的最适工艺参数是浸提剂乙醇浓度为70%,提取温度为50℃,液料比为20：1,提取时间为20 min,且总黄酮提取率可达4.458%。     

Determination of ebrotidine and its metabolites in human urine by reversed-phase ion-pair high-performance liquid chromatography

Ebrotidine is a new H₂-receptor antagonist with powerful antisecretory activity, demonstrated gastroprotection and the ability to inhibit protease and lipase activities of Helicobacter pylori. As a tool in the clinical pharmacokinetic study of ebrotidine, an analytical method for the simultaneous determination of ebrotidine an its metabolites in human urine was developed. An ion-pair reversed-phase HPLC separation using 1-hexanesulfonic acid and acetonitrile as mobile phase with gradient elution was optimized. In addition, several procedures of preconcentration and clean-up were tested, including solid-phase and liquid—liquid extraction, the mixture dichloromethane—2-propanol (9:1, v/v) at pH 11 being the most efficient. The quality parameters of the whole analytical method were established, the calibration curves were linear over the range studied (1–200 μg/ml) and the reproducibility of the method was high (inter-day R.S.D. values lower than 4.4%).The limits of detection were between 26 and 110 ng/ml of urine for ebrotidine and its metabolites. The method was applied to the analysis of urine collected from two volunteers during 96 h following oral administration of ebrotidine at a dose of 400 mg.     

UHPLC method for the simultaneous determination of β-blockers, isoflavones and their metabolites in human urine

A rapid-resolution ultra high-performance liquid chromatography separation method (UHPLC) for the simultaneous determination of the following β-blockers: milrinone, sotalol, metoprolol, propranolol and carvedilol, and their metabolites: 5′-hydroxylphenyl-carvedilol, O-desmethylcarvedilol, 4-hydroxypropranolol, α-hydroxy-metoprolol, O-desmethyl-metoprolol; the following isoflavones: genistein, daidzein, glycitin, glycitein, puerarin and biochanin A; as well as their metabolites: dihydrogenistein, desmethylglycitein, 8-hydroxygenistein, daidzein-7,4′-diglucoside, 8-hydroxydaidzein, dihydrobiochanin A in human urine was optimized. The analysed compounds were extracted from human urine by means of solid phase extraction (SPE). The effective UHPLC separation of the examined compounds was applied on a Hypersil GOLD? (50 mm × 2.1 mm, 1.9 μm) column with a gradient mobile phase system and a UV detector. The complete separation of all analytes was achieved within 8.0 min. The method was validated for the determination of the aforementioned substances in human urine. The linear ranges, limits of detection (LOD) and limits of quantification (LOQ) for β-blockers, isoflavones and their metabolites were determined. The intra- and inter-day precision (%C.V.) was less than 4.48%, and the intra-day and inter-day accuracy was less than 4.74%. The tested SPE sorbent proved that appropriate absolute recoveries can be obtained for Oasis HLB (Waters). The mean recovery of the analytes, using the new SPE procedure, amounted from 70.14% to 99.85%. The present paper reports, for the first time, the method for the determination of β-blockers, isoflavones and their metabolites in human urine samples. The newly developed method was suitably validated and successfully applied for the analysis of the certain of the aforementioned analytes in human urine samples obtained from the patients suffering cardiovascular disease.     

Enantioselective high-performance liquid chromatographic method for the determination of methadone and its main metabolite in urine using an AGP and a C8 column coupled serially

A simple and sensitive method for the enantioselective high-performance liquid chromatographic determination of methadone and its main metabolite, EDDP, in human urine is described. (−)-(R)-Methadone, (+)-(S)-methadone, (+)-(R)-EDDP, (−)-(S)-EDDP and imipramine as an internal standard are detected by ultraviolet detection at 200 nm. The enantiomers of methadone and EDDP were extracted from human urine by a simple liquid–liquid extraction procedure. The extracted sample was reconstructed in mobile phase and the enantiomers of methadone and EDDP were quantitatively separated by HPLC on a short analytical LiChrospher RP8 column coupled in series with a chiral AGP column. Determination of all four enantiomers was possible in the range of 0.03 to 2.5 μM. The recoveries of methadone enantiomers and EDDP enantiomers added to human urine were about 90% and 80%, respectively. The method was applicable for determination of methadone enantiomers and the enantiomers of its main metabolite in urine samples from methadone maintenance patients and patients suffering from severe chronic pain.     

Determination of melamine and cyanuric acid in human urine by a liquid chromatography tandem mass spectrometry

Melamine was found to be the etiological factor for the urinary stones epidemic in infants and young children in China in 2008. Urine level of melamine and its analog cyanuric acid may be useful markers for the evaluation of toxic effects. Liquid chromatography tandem mass spectrometry methods for the individual determination of melamine and cyanuric acid in human urine are described. Using isotope labeled internal standards during liquid–liquid extraction, the method was fully validated by verifying specificity, linearity, LLOQ, intra- and inter-assay precision and accuracy, matrix effect, recovery and stability. Calibration curves with good linearity (r = 0.9999) over the concentration range from 10 to 5000 ng/ml, intra-assay precision <10% and inter-assay precision <15%, accuracy between 93.0 and 111.6% were obtained with multiple reaction monitoring mode for melamine and cyanuric acid in human urine. The methods were successfully applied to the analysis of urine samples collected from 86 infants and 110 adults.