GC/MS analysis of the rat urine for metabonomic research

In this paper, an optimized protocol was established and validated for the metabonomic profiling in rat urine using GC/MS. The urine samples were extracted by methanol after treatment with urease to remove excessive urea, then the resulted supernatant was dried, methoximated, trimethylsilylated, and analyzed by GC/MS. Forty-nine endogenous metabolites were separated and identified in GC/MS chromatogram, of which 26 identified compounds were selected for quantitative analysis to evaluate the linearity, precision, and sensitivity of the method. It showed good linearity between mass spectrometry responses and relative concentrations of the 26 endogenous compounds over the range from 0.063 to 1.000 (v/v, urine/urine+water) and satisfactory reproducibility with intra-day and inter-days precision values all below 15%. The metabonomic profiling method based on GC/MS was successfully applied to urine samples from hyperlipidemia model rats. Obviously, separated clustering of model rats and the control rats were shown by principal components analysis (PCA); time-dependent metabonomic modification was detected as well. It was suggested that metabonomic profiling based on GC/MS be a robust method for urine samples.     

Within-day reproducibility of an HPLC-MS-based method for metabonomic analysis: application to human urine

Self-evidently, research in areas supporting "systems biology" such as genomics, proteomics, and metabonomics are critically dependent on the generation of sound analytical data. Metabolic phenotyping using LC-MS-based methods is currently at a relatively early stage of development, and approaches to ensure data quality are still developing. As part of studies on the application of LC-MS in metabonomics, the within-day reproducibility of LC-MS, with both positive and negative electrospray ionization (ESI), has been investigated using a standard "quality control" (QC) sample. The results showed that the first few injections on the system were not representative, and should be discarded, and that reproducibility was critically dependent on signal intensity. On the basis of these findings, an analytical protocol for the metabonomic analysis of human urine has been developed with proposed acceptance criteria based on a step-by-step assessment of the data. Short-term sample stability for human urine was also assessed. Samples were stable for at least 20 h at 4 degrees C in the autosampler while queuing for analysis. Samples stored at either -20 or -80 degrees C for up to 1 month were indistinguishable on subsequent LC-MS analysis. Overall, by careful monitoring of the QC data, it is possible to demonstrate that the "within-day" reproducibility of LC-MS is sufficient to ensure data quality in global metabolic profiling applications.     

High temperature-ultra performance liquid chromatography-mass spectrometry for the metabonomic analysis of Zucker rat urine

The applicability and potential of using elevated temperatures and sub 2-microm porous particles in chromatography for metabonomics/metabolomics was investigated using, for the first time, solvent temperatures higher than the boiling point of water (up to 180 degrees C) and thermal gradients to reduce the use of organic solvents. Ultra performance liquid chromatography, combined with mass spectrometry, was investigated for the global metabolite profiling of the plasma and urine of normal and Zucker (fa/fa) obese rats (a well established disease animal model). "Isobaric" high temperature chromatography, where the temperature and flow rate follow a gradient program, was developed and evaluated against a conventional organic solvent gradient. LC-MS data were first examined by established chromatographic criteria in order to evaluate the chromatographic performance and next were treated by special peak picking algorithms to allow the application of multivariate statistics. These studies showed that, for urine (but not plasma), chromatography at elevated temperatures provided better results than conventional reversed-phase LC with higher peak capacity and better peak asymmetry. From a systems biology point of view, better group clustering and separation was obtained with a larger number of variables of high importance when using high temperature-ultra performance liquid chromatography (HT-UPLC) compared to conventional solvent gradients.     

Normalization strategies for cDNA microarrays

Multiple Arabidopsis thaliana clones from an experimental series of cDNA microarrays are evaluated in order to identify essential sources of noise in the spotting and hybridization process. Theoretical and experimental strategies for an improved quantitative evaluation of cDNA microarrays are proposed and tested on a series of differently diluted control clones. Several sources of noise are identified from the data. Systematic and stochastic fluctuations in the spotting process are reduced by control spots and statistical techniques. The reliability of slide to slide comparison is critically assessed within the statistical framework of pattern matching and classification.     

Normalization techniques for PARAFAC modeling of urine metabolomic data

Introduction

One of the body fluids often used in metabolomics studies is urine. The concentrations of metabolites in urine are affected by hydration status of an individual, resulting in dilution differences. This requires therefore normalization of the data to correct for such differences. Two normalization techniques are commonly applied to urine samples prior to their further statistical analysis. First, AUC normalization aims to normalize a group of signals with peaks by standardizing the area under the curve (AUC) within a sample to the median, mean or any other proper representation of the amount of dilution. The second approach uses specific end-product metabolites such as creatinine and all intensities within a sample are expressed relative to the creatinine intensity.

Objectives

Another way of looking at urine metabolomics data is by realizing that the ratios between peak intensities are the information-carrying features. This opens up possibilities to use another class of data analysis techniques designed to deal with such ratios: compositional data analysis. The aim of this paper is to develop PARAFAC modeling of three-way urine metabolomics data in the context of compositional data analysis and compare this with standard normalization techniques.

Methods

In the compositional data analysis approach, special coordinate systems are defined to deal with the ratio problem. In essence, it comes down to using other distance measures than the Euclidian Distance that is used in the conventional analysis of metabolomic data.

Results

We illustrate using this type of approach in combination with three-way methods (i.e. PARAFAC) of a longitudinal urine metabolomics study and two simulations. In both cases, the advantage of the compositional approach is established in terms of improved interpretability of the scores and loadings of the PARAFAC model.

Conclusion

For urine metabolomics studies, we advocate the use of compositional data analysis approaches. They are easy to use, well established and proof to give reliable results.

     

Untargeted metabolomic analysis of urine samples for diagnosis of inherited metabolic disorders

Functional & Integrative Genomics - Metabolomics has become an important tool for clinical research, especially for analyzing inherited metabolic disorders (IMDs). The purpose of this study was...     

Holistic metabonomic profiling of urine affords potential early diagnosis for bladder and kidney cancers

The clinical exploration of urinary metabonomic analysis on discriminating between the top-two-incidence urological cancers, bladder and kidney cancers (BC and KC), is still virgin land. In this study, we discovered and evaluated the clinical utility of holistic metabonomic profiling and current single biomarker methods, and ultimately suggested a potential screening test for BC and KC. Urine metabonomic profiling for 19 BC patients, 25 KC patients, and 24 healthy controls was carried out using an LC–MS based platform, which utilized both reversed phase chromatography and hydrophilic interaction chromatography. The holistic method that refers to orthogonal partial least-squares-discriminant analysis based on all qualified profile data, successfully classified BC, KC and healthy control groups, showing 100 % sensitivity and specificity. Taurine, hippuric acid, phenylacetylglutamine and carnitine species contributed most to the BC and KC discrimination. The predictive power of each above metabolite is evaluated using receiver operator characteristic technique. Hippuric acid was found 10-fold decrease in concentration relative healthy controls, and performed the best as a biomarker for BC diagnosis, with its sensitivity and specificity of 78.9 and 86.5 %, respectively. Carnitine C10:3 was found 1.5-fold decrease, and reached 84.0 % of sensitivity and 60.5 % of specificity for KC diagnosis. In view of both sensitivity and specificity, the holistic method is more accurate for detecting BC and KC, than current single metabonomic biomarker methods, and it could be advocated as a prescreen to other forms of more invasive or uncomfortable screening. Moreover, this approach also demonstrates attractive performance in diagnosis of early stage (ES) BC and KC patients.     

Development and comparative analysis of human urine exosome isolation strategies

Exosomes contain virtually every type of biomolecules that have originated from parental cells. High concentrations of exosomes are found in a variety of body fluids including urine, a body fluid that can be easily and non-invasively collected. Therefore, urinary exosomes are ideal materials for liquid biopsy. Although there are some major barriers to their use which include high variability and lack of standarization of exosome isolation methods. Therefore, it is highly recommended to systemically assess urinary exosome isolation strategies in terms of isolation concentration and purity. In this study, comparative studies among eight different strategies based on ultracentrifugation, ultrafiltration, precipitation, and size exclusion chromatography (SEC) were performed for urinary exosome isolation from healthy donors. The results indicated that SEC combined with ultrafiltration was the most compromised and balanced method for urinary exosome isolation in terms of both isolation concentration and purity. SEC combined with precipitation yielded the highest purity. Thus, the appropriate urinary exosome isolation method can be chosen depending on the downstream applications of isolated urinary exosomes. This comparative analysis of urinary exosome isolation methods contributes to the discovery of exosome-associated biomarker and the development of exosome-based diagnostics.     

Method development in high-performance liquid chromatography for high-throughput profiling and metabonomic studies of biofluid samples

"Metabonomics" has in the past decade demonstrated enormous potential in furthering the understanding of, for example, disease processes, toxicological mechanisms, and biomarker discovery. The same principles can also provide a systematic and comprehensive approach to the study of food ingredient impact on consumer health. However, "metabonomic" methodology requires the development of rapid, advanced analytical tools to comprehensively profile biofluid metabolites within consumers. Until now, NMR spectroscopy has been used for this purpose almost exclusively. Chromatographic techniques and in particular HPLC, have not been exploited accordingly. The main drawbacks of chromatography are the long analysis time, instabilities in the sample fingerprint and the rigorous sample preparation required. This contribution addresses these problems in the quest to develop generic methods for high-throughput profiling using HPLC. After a careful optimization process, stable fingerprints of biofluid samples can be obtained using standard HPLC equipment. A method using a short monolithic column and a rapid gradient with a high flow-rate has been developed that allowed rapid and detailed profiling of larger numbers of urine samples. The method can be easily translated into a slow, shallow-gradient high-resolution method for identification of interesting peaks by LC-MS/NMR. A similar approach has been applied for cell culture media samples. Due to the much higher protein content of such samples non-porous polymer-based small particle columns yielded the best results. The study clearly shows that HPLC can be used in metabonomic fingerprinting studies.     

Normalization and calculation of lanthanide element concentrations in environmental samples

Summary A mathematical model for the prediction of lanthanide element concentrations in soil and plant samples is presented. A comparison between pre dicted and measured lanthanide values in soil and plant samples show, that the model produces good results for the elements in the soil samples and for most elements in plant material. The accuracy of prediction worsens with decreasing concentration of the heavier lanthanide elements. The mathematical model presented is not valid on other environmental samples like aerosols, because no data for these matrices are available yet to calibrate our normalized curves.     

Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples

Serum proteins may often serve as indicators of disease and is a rich source for biomarker discovery. However, the large dynamic range of proteins in serum makes the analysis very challenging because high-abundant proteins tend to mask those of lower abundance. A prefractionation step, such as depletion of a few high-abundant proteins before protein profiling, can assist in the discovery and detection of less abundant proteins that may prove to be informative biomarkers. In the present study, five different depletion columns were investigated considering efficiency, specificity, and reproducibility. Our research included quantitative determination of total protein, albumin, and immunoglobulin G (IgG) concentrations, one- and two-dimensional gels and mass spectrometric analysis of the serum samples before and after the depletion step. Our results showed that all five depletion columns tested removed albumin and IgG with high efficiency. We found that based on reproducibility and binding specificity, the Multiple Affinity Removal Column that removed a total of six high-abundant proteins (albumin, IgG, antitrypsin, IgA, transferring, and haptoglobin) offered the most promising depletion approach. Among the disposable (single-use) products, the ProteoExtract Albumin/IgG Removal kit displayed the best results. Depleted serum from the Multiple Affinity Removal column was further evaluated by 2-D gel electrophoresis (2-DE) analysis, and the results indicated increased resolution and improved intensity of low-abundant proteins in a reproducible fashion. Our study provides a comprehensive investigation of commercially available depletion columns and will be of high importance for future proteomic studies on serum samples.     

Adaptive strategies for post-renal handling of urine in birds

Birds are a diverse vertebrate class in terms of diet and habitat, but they share several common physiological features, including the use of uric acid as the major nitrogenous waste product and the lack of a urinary bladder. Instead, ureteral urine refluxes from the urodeum into the more proximal coprodeum and portions of the hindgut (colon or rectum and ceca). This presents a potential problem in that hyperosmotic ureteral urine in contact with the permeable epithelia of these tissues would counteract renal osmotic work. This review describes and provides examples of different strategies used by avian species to balance renal and post-renal changes in urine composition. The strategies described include: 1. a "reptilian" mode, with moderate renal concentrating ability, but high rates of post-renal salt and water resorption; 2. the "mammalian" strategy, in which the coprodeum effectively functions like a mammalian urinary bladder, preserving the osmotic concentrating work of the kidney; 3. an interaction strategy, in which post-renal transport processes are hormonally regulated in order to optimize renal function under varying conditions of salt or water stress; 4. the salt gland strategy seen in marine or estuarine birds with functional salt glands, in which post-renal transport mechanisms are used to conserve urinary water and to recycle excess NaCl to the nasal salt glands. Finally, we also describe some features of an as-yet unstudied group of birds, the birds of prey. At least some species in this group are relatively good renal concentrators, and would be predicted to have post-renal mechanisms to preserve this work. This new synthesis illustrates the marked diversity of adaptive mechanisms used by avian species to maintain osmotic homeostasis.     

A novel R-package graphic user interface for the analysis of metabonomic profiles

Background  

Analysis of the plethora of metabolites found in the NMR spectra of biological fluids or tissues requires data complexity to be simplified. We present a graphical user interface (GUI) for NMR-based metabonomic analysis. The "Metabonomic Package" has been developed for metabonomics research as open-source software and uses the R statistical libraries.     

LC-MS analysis of trimethoxyamphetamine designer drugs (TMA series) from urine samples

A sensitive liquid chromatography-mass spectrometric (LC-MS) method for quantification of an active psychedelic hallucinogenic drugs (trimethoxyamphetamines) in human urine after solid-phase extraction (SPE) with C(18) cartridge was developed and validated. Chromatographic separation was achieved on reversed-phase Phenomenex 3.0 microm Polar Plus column (150 mm x 2.1 mm) with acetonitrile -0.2% acetic acid as mobile-phase and the step gradient elution resulted in a total run time of about 20 min. The analytes were detected by using an electrospray positive ionization mass spectrometry in selected ion monitoring (SIM) mode. In the evaluated concentration range (10-200 ng/mL) (R(2) > or = 0.998) a good linear relationship was obtained. The lower limits of detection (LLODs) and quantification (LLOQs) ranged from 4.26 to 9.12 ng/mL and from 13.18 to 29.22 ng/mL, respectively. Average recoveries ranged from 68.52 to 97.90% in urine at the concentrations of 25, 50 and 100 ng/mL. Intra- and inter-day relative standard deviations were 3.70-10.77% and 7.63-12.94%, respectively. This LC-MS method proved to be robust and reliable, and suitable for the use as a confirmation method in clinical urine drug testing.     

Evaluation of methods for determining N-acetyl-beta-D-glucosaminidase in urine of rats without purification of urine samples.

N-Acetyl-beta-D-glucosaminidase (NAG) activities in urine of rats were measured with methods recommended as procedures without the pretreatment of urine sample. Four different derivatives [4-nitrophenyl; 3-cresolsulfonephthaleinyl; 3,3'-dichlorophenylsulfonephthaleinyl; 2-methoxy-4-(2-nitrovinyl)phenyl] of N-acetyl-beta-D-glucosaminide were compared for determination. The conventional test using the 4-nitrophenyl derivative showed the highest activities and was very well correlated with the other tests. The test using the 3,3'-dichlorophenylsulfonephthaleinyl substrate is most convenient and practical to determine NAG in small animals because it is, in contrast to the other three discontinuous (endpoint) tests, a continuous (kinetic) assay which can be easily adapted to clinical chemistry analyzers.     

Immunodiagnosis of alveolar echinococcosis using urine samples

Alveolar echinococcosis (AE) is one of the most lethal zoonotic parasitic infections. The diagnosis is based on the combination of the abdominal imaging including CT, MRI and PET, and serology. To develop a new diagnostic tool for AE with urine as samples, mouse-Echinococcus multilocularis (Em) model and then human cases were studied. The antibody levels of urine and serum samples from the infected mice and AE cases were well correlated with each other. The sensitivity and specificity of the method with urine were 91% and 98%, respectively, when IgG4 to crude Em was examined. Comparing with serum samples, the collection of urine is easier and safer and the urine diagnostic tool makes surveys of this silent disease easier.     

Capillary zone electrophoresis with diode-array detection for analysis of local anaesthetics and opium alkaloids in urine samples

The present study describes the simultaneous determination of four drugs, two local anaesthetics (lidocaine and bupivacaine) and two opium alkaloids (noscapine and papaverine) by capillary zone electrophoresis (CZE) with solid-phase extraction (SPE) procedure using Oasis HLB cartridges. Their recoveries ranged from 81 to 107% at the target concentrations of 2.0, 5.0 and 8.0 μg mL^?1 in spiked urine samples. Coefficients of variation of the recoveries ranged from 2.1 to 11.3% at these concentrations. The quantitation limits of the method were approximately 300 ng mL^?1 for the different compounds studied. The assay is very specific for these compounds and requires a short sample preparation procedure prior to the electrophoretic analysis.     

2D NMR metabonomic analysis: a novel method for automated peak alignment

MOTIVATION: Comparative metabolic profiling by nuclear magnetic resonance (NMR) is showing increasing promise for identifying inter-individual differences to drug response. Two dimensional (2D) (1)H (13)C NMR can reduce spectral overlap, a common problem of 1D (1)H NMR. However, the peak alignment tools for 1D NMR spectra are not well suited for 2D NMR. An automated and statistically robust method for aligning 2D NMR peaks is required to enable comparative metabonomic analysis using 2D NMR. RESULTS: A novel statistical method was developed to align NMR peaks that represent the same chemical groups across multiple 2D NMR spectra. The degree of local pattern match among peaks in different spectra is assessed using a similarity measure, and a heuristic algorithm maximizes the similarity measure for peaks across the whole spectrum. This peak alignment method was used to align peaks in 2D NMR spectra of endogenous metabolites in liver extracts obtained from four inbred mouse strains in the study of acetaminophen-induced liver toxicity. This automated alignment method was validated by manual examination of the top 50 peaks as ranked by signal intensity. Manual inspection of 1872 peaks in 39 different spectra demonstrated that the automated algorithm correctly aligned 1810 (96.7%) peaks. AVAILABILITY: Algorithm is available upon request.