LC-MS-based metabonomics analysis. J Chromatogr B Analyt Technol Biomed Life Sci. 2008;866:64-76. [PMID: 17983864 DOI: 10.1016/j.jchromb.2007.10.022]

The potential of metabolomics for Leishmania research in the post-genomics era

The post-genomics era has provided researchers with access to a new generation of tools for the global characterization and understanding of pathogen diversity. This review provides a critical summary of published Leishmania post-genomic research efforts to date, and discusses the potential impact of the addition of metabolomics to the post-genomic toolbox. Metabolomics aims at understanding biology by comprehensive metabolite profiling. We present an overview of the design and interpretation of metabolomics experiments in the context of Leishmania research. Sample preparation, measurement techniques, and bioinformatics analysis of the generated complex datasets are discussed in detail. To illustrate the concepts and the expected results of metabolomics analyses, we also present an overview of comparative metabolic profiles of drug-sensitive and drug-resistant Leishmania donovani clinical isolates.

Multitarget quantitative metabolic profiling of hydrophilic metabolites in fermentation broths of β-lactam antibiotics production by HILIC-ESI-MS/MS

The presented work deals with the development and comprehensive validation of a quantitative LC-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) method using a triple quadrupole instrument in the MRM mode for the metabolic profiling of amino acids, organic acids, vitamins, some biogenic amines, secondary metabolites of β-lactam antibiotics biosynthesis as well as their intermediates, and degradation products in fermentation broths of β-lactam antibiotics production (in total 57 hydrophilic compounds). A great number of chromatographic systems (22 different stationary phase/mobile phase conditions) were screened for their adequate chromatographic selectivity to cope with isobaric compounds and other critical analyte pairs. Finally, a hydrophilic interaction liquid chromatography (HILIC) method employing a zwitterionic ZIC-HILIC column was selected as best compromise. Particular focus was given on the elucidation of absolute and relative matrix effects via comparison of slopes of calibration functions of spiked matrix and standard solutions. These data as well as precision and accuracy data confirm suitability of the HILIC-ESI-MS/MS assay for metabolic profiling studies in fermentation samples. Detailed comprehensive data sets are presented which should illustrate critical issues, problems, and challenges of multitarget quantitative metabolic profiling and should outline possible strategies to circumvent pitfalls and overcome common problems.

Plasma phospholipid metabolic profiling and biomarkers of rats following radiation exposure based on liquid chromatography-mass spectrometry technique

Lipidomics, a prominent area of metabolomics, utilizes novel analytical methodologies to study the extensive classes of lipid molecules, changes in lipid metabolism and lipid-mediated signaling processes. In this paper, the phospholipid metabolic profiles changes and potential biomarker identification in the rats plasma after gamma-irradiation exposure were investigated by coupling high performance liquid chromatography-mass spectrometry technology to multivariate statistical analysis. Orthogonal partial least-squares to latent structures discriminate analysis (OPLS-DA) was used to find the potential plasma phospholipids biomarkers of rats for radiation exposure. According to the corresponding tandem mass spectrometric results, potential biomarkers were identified. After exposure to gamma-rays, phosphatidylethanolamine and phosphatidylserine showed a marked increase, and phosphatidylcholine, sphingomyelin and lysophosphatidylcholine followed the same trend, although their rise was not significant. The results suggested that radiated rats had a phospholipid metabolic abnormality, which could be an alternative way to assess the radiaton exposure. The biomarkers may involve a radiation-induced apoptosis pathway and represent a promising target for discovery new radioprotective drugs and radiosensitizers.

Metabolic profiling of intracellular metabolites in fermentation broths from beta-lactam antibiotics production by liquid chromatography-tandem mass spectrometry methods

An analytical platform comprising three LC-ESI-MS/MS methods is presented for qualitative and quantitative profiling of more than 200 intracellular metabolites. Employing a silica based zwitterionic stationary phase in the HILIC mode, in total 223 hydrophilic metabolites can be determined. In particular, amino acids, organic acids as well as nucleotide sugars were found to be well separable and detectable under acidic mobile phase conditions, while in comparison especially phosphates such as nucleotides, coenzymes or sugar phosphates as well as sugars and sugar acids performed better at higher pH. Additionally, 21 less polar analytes turned out to be amenable for separation and analysis on a pentafluorophenyl modified silica stationary phase in RP mode. Solutes were detected by tandem mass spectrometry on a triple quadrupole instrument in the selected reaction monitoring (SRM) mode and specific SRM transitions for 258 metabolites are provided. All three methods were validated with respect to the limit of quantification, linear dynamic range, precision and accuracy. Applicability of the analytical platform was evaluated by analysis of the targeted metabolites in extracts of beta-lactam antibiotics fermentation broths. Thereby, 87 metabolites were determined qualitatively in penicillin fermentation broths, and 94 compounds were found in cephalosporin extracts. In addition, a number of selected metabolites that can be determined by at least two of the presented LC-MS/MS methods was analyzed quantitatively by both, external calibration using pure standards as well as by matrix-matched calibration performing standard addition. Quantitative results obtained with the different methods agreed well, however, for some analytes external calibration was found to be ill-suited due to matrix effects.

Development of extractive electrospray ionization ion trap mass spectrometry for in vivo breath analysis

In metabolomics studies and clinical diagnosis, interest is increasing in the rapid analysis of exhaled breath. In vivo breath analysis offers a unique, unobtrusive, non-invasive method of investigating human metabolism. To analyze breath in vivo, we constructed a novel platform of extractive electrospray ionization (EESI) ion trap mass spectrometry (ITMS) using a home-made EESI source coupled to a linear trap quadrupole mass spectrometer. A reference compound (authentic n-octyl amine) was used to evaluate effects of systematically varying selected characteristics of the EESI source on signal intensity. Under the optimized working conditions, metabolic changes of human bodies were in vivo followed by performing rapid breath analysis using the multi-stage EESI-ITMS tandem mass spectrometry platform. For nicotine, a limit of determination was found to be 0.05 fg mL(-1) (S/N = 3, RSD = 5.0 %, n = 10) for nicotine in aerosol standard samples; the dynamic response range was from 0.0155 pg mL(-1) to 155 pg mL(-1). The concentration of nicotine in the exhaled breath of a regular smoker was in vivo determined to be 5.8 pg mL(-1), without any sample pre-treatment. Our results show that EESI-ITMS is a powerful analytical platform to provide high sensitivity, high specificity and high throughput for semi-quantitative analysis of complex samples in life science, particularly for in vivo metabolomics studies.

A metabonomic approach to early prognostic evaluation of experimental sepsis by (1)H NMR and pattern recognition

This study proposes an NMR-based metabonomic approach to early prognostic evaluation of sepsis. Forty septic rats receiving cecal ligation and puncture (CLP) were divided into the surviving group and nonsurviving group on day 6, while 20 sham-operated rats served as the control group. Serum samples were collected from septic and sham-operated rats at 12 h after surgery and analyzed using (1)H NMR spectroscopy. Orthogonal partial least squares (OPLS) were applied and showed clustering according to predefined groups, indicating that NMR-based metabolic profiling could reveal pathologic characteristics in the serum of sham-operated, surviving, and nonsurviving septic rats. In addition, six characteristic metabolites including lactate, alanine, acetate, acetoacetate, hydroxybutyrate, and formate, which are mainly involved in energy metabolism, changed markedly in septic rats, especially in the nonsurvivors. Using these metabolites, a predictive model for prognostic evaluation of sepsis was constructed using a radial basis function neural network (RBFNN) with a prediction accuracy of about 87% by test samples. The results indicated that the NMR-based metabonomic approach is a potential technique for the early prognostic evaluation of sepsis.

Application of metabonomic analytical techniques in the modernization and toxicology research of traditional Chinese medicine

In the recent years, a wide range of metabonomic analytical techniques are widely used in the modern research of traditional Chinese medicine (TCM). At the same time, the international community has attached increasing importance to TCM toxicity problems. Thus, many studies have been implemented to investigate the toxicity mechanisms of TCM. Among these studies, many metabonomic-based methods have been implemented to facilitate TCM toxicity investigation. At present, the most prevailing methods for TCM toxicity research are mainly single analysis techniques using only one analytical means. These techniques include nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), and liquid chromatography-mass spectrometry (LC-MS), etc.; with these techniques, some favourable outcomes have been gained in the toxic reaction studies of TCM, such as the action target organs assay, the establishment of action pattern, the elucidation of action mechanism and the exploration of action material foundation. However, every analytical technique has its advantages and drawbacks, no existing analytical technique can be versatile. Multi-analysed techniques can partially overcome the shortcomings of single-analysed techniques. Combination of GC-MS and LC-MS metabolic profiling approaches has unravelled the pathological outcomes of aristolochic acid-induced nephrotoxicity, which can not be achieved by single-analysed techniques. It is believed that with the further development of metabonomic analytical techniques, especially multi-analysed techniques, metabonomics will greatly promote TCM toxicity research and be beneficial to the modernization of TCM in terms of extending the application of modern means in the TCM safety assessment, assisting the formulation of TCM safety norms and establishing the international standards indicators.

apLCMS--adaptive processing of high-resolution LC/MS data

MOTIVATION

Liquid chromatography-mass spectrometry (LC/MS) profiling is a promising approach for the quantification of metabolites from complex biological samples. Significant challenges exist in the analysis of LC/MS data, including noise reduction, feature identification/ quantification, feature alignment and computation efficiency.

RESULT

Here we present a set of algorithms for the processing of high-resolution LC/MS data. The major technical improvements include the adaptive tolerance level searching rather than hard cutoff or binning, the use of non-parametric methods to fine-tune intensity grouping, the use of run filter to better preserve weak signals and the model-based estimation of peak intensities for absolute quantification. The algorithms are implemented in an R package apLCMS, which can efficiently process large LC/ MS datasets.

AVAILABILITY

The R package apLCMS is available at www.sph.emory.edu/apLCMS.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Metabonomics study of liver cancer based on ultra performance liquid chromatography coupled to mass spectrometry with HILIC and RPLC separations

In this study, urinary metabolites from liver cancer patients and healthy volunteers were studied by a metabonomic method based on ultra performance liquid chromatography coupled to mass spectrometry. Both hydrophilic interaction chromatography (HILIC) and reversed-phase liquid chromatography (RPLC) were used to separate the urinary metabolites. Principle component analysis (PCA) and partial least squares to latent structure-discriminant analysis (PLS-DA) models were built to separate the healthy volunteers from the liver cancer patients and to find compounds that are expressed in significantly different amounts between the two populations. 21 metabolite ions were considered as potential biomarkers according to the Variable importance in the Project (VIP) value and S-plot. Compared with RPLC, a more sensitive and stable response can be recorded in HILIC mode due to the high content of organic solvent used. Moreover, the liver cancer group and the healthy volunteers can be better separated based on the data from the HILIC separation, which indicates that HILIC is suitable for urinary metabonomic analysis. In HILIC mode, several polar compounds related to arginine and proline metabolism, alanine and aspartate metabolism, lysine degradation, nicotinate and nicotinamide metabolism were found to be significantly changed in the concentrations of the two different populations: healthy and cancer. In contrast, in RPLC mode, these changed compounds are related to fatty acids oxidation.

Metabonomics research of diabetic nephropathy and type 2 diabetes mellitus based on UPLC-oaTOF-MS system

Ultra performance liquid chromatography (UPLC) coupled with orthogonal acceleration time-of-flight (oaTOF) mass spectrometry has showed great potential in diabetes research. In this paper, a UPLC-oaTOF-MS system was employed to distinguish the global serum profiles of 8 diabetic nephropathy (DN) patients, 33 type 2 diabetes mellitus (T2DM) patients and 25 healthy volunteers, and tried to find potential biomarkers. The UPLC system produced information-rich chromatograms with typical measured peak widths of 4 s, generating peak capacities of 225 in 15 min. Furthermore, principal component analysis (PCA) was used for group differentiation and marker selection. As shown in the scores plot, the distinct clustering between the patients and controls was observed, and DN and T2DM patients were also separated into two individual groups. Several compounds were tentatively identified based on accurate mass, isotopic pattern and MS/MS information. In addition, significant changes in the serum level of leucine, dihydrosphingosine and phytosphingosine were noted, indicating the perturbations of amino acid metabolism and phospholipid metabolism in diabetic diseases, which having implications in clinical diagnosis and treatment.

Automated molecular formula determination by tandem mass spectrometry (MS/MS)

Automated software was developed to analyze the molecular formula of organic molecules and peptides based on high-resolution MS/MS spectroscopic data. The software was validated with 96 compounds including a few small peptides in the mass range of 138-1569 Da containing the elements carbon, hydrogen, nitrogen and oxygen. A Micromass Waters Q-TOF Ultima Global mass spectrometer was used to measure the molecular masses of precursor and fragment ions. Our software assigned correct molecular formulas for 91 compounds, incorrect molecular formulas for 3 compounds, and no molecular formula for 2 compounds. The obtained 95% success rate indicates high reliability of the software. The mass accuracy of the precursor ion and the fragment ions, which is critical for the success of the analysis, was high, i.e. the accuracy and the precision of 850 data were 0.0012 Da and 0.0016 Da, respectively. For the precursor and fragment ions below 500 Da, 60% and 90% of the data showed accuracy within < or = 0.001 Da and < or = 0.002 Da, respectively. The precursor and fragment ions above 500 Da showed slightly lower accuracy, i.e. 40% and 70% of them showed accuracy within < or = 0.001 Da and < or = 0.002 Da, respectively. The molecular formulas of the precursor and the fragments were further used to analyze possible mass spectrometric fragmentation pathways, which would be a powerful tool in structural analysis and identification of small molecules. The method is valuable in the rapid screening and identification of small molecules such as the dereplication of natural products, characterization of drug metabolites, and identification of small peptide fragments in proteomics. The analysis was also extended to compounds that contain a chlorine or bromine atom.

Changes of the plasma metabolome during an oral glucose tolerance test: is there more than glucose to look at?

The oral glucose tolerance test (oGTT) is a common tool to provoke a metabolic challenge for scientific purposes, as well as for diagnostic reasons, to monitor the kinetics of glucose and insulin. Here, we aimed to follow the variety of physiological changes of the whole metabolic pattern in plasma during an oGTT in healthy subjects in a nontargeted reversed-phase ultra performance liquid chromatography coupled to electrospray ionization quadrupole time of flight mass spectrometric metabolomics approach. We detected 11,500 metabolite ion masses/individual. Applying multivariate data analysis, four major groups of metabolites have been detected as the most discriminating oGTT biomarkers: free fatty acids (FFA), acylcarnitines, bile acids, and lysophosphatidylcholines. We found in detail 1) a strong decrease of all saturated and monounsaturated FFA studied during the oGTT; 2) a significant faster decline of palmitoleate (C16:1) and oleate (C18:1) FFA levels than their saturated counterparts; 3) a strong relative increase of polyunsaturated fatty acids in the fatty acid pattern at 120 min; and 4) a clear decrease in plasma C10:0, C12:0, and C14:1 acylcarnitine levels. These data reflect the switch from beta-oxidation to glycolysis and fat storage during the oGTT. Moreover, the bile acids glycocholic acid, glycochenodeoxycholic acid, and glycodeoxycholic acid were highly discriminative, showing a biphasic kinetic with a maximum of a 4.5- to 6-fold increase at 30 min after glucose ingestion, a significant decrease over the next 60 min followed by an increase until the end of the oGTT. Lysophosphatidylcholines were also increased significantly. The findings of our metabolomics study reveal detailed insights in the complex physiological regulation of the metabolism during an oGTT offering novel perspectives of this widely used procedure.

Metabonomic study of biochemical changes in the serum of type 2 diabetes mellitus patients after the treatment of metformin hydrochloride

A metabonomic study on biochemical changes in the serum of type 2 diabetes mellitus patients after the treatment of metformin hydrochloride was performed. (1)H NMR and UPLC/MS were used to generate metabolic fingerprints for the metabonomic analysis of serum samples obtained from 20 type 2 diabetes mellitus patients without any drugs treatment and 15 type 2 diabetes mellitus patients treated with metformin hydrochloride for 3 months. The resulting data were subjected to chemometric analysis (principal component analysis and partial least squares discriminant analysis) to investigate the effect of metformin hydrochloride on serum metabolite profiles of type 2 diabetes mellitus patients. (1)H NMR spectroscopic analysis revealed increased trimethylamine-N-oxide (TMAO), 3-hydroxybutyrate (3-HB) and decreased glucose, N-acetyl glycoprotein (NAC), lipoprotein, lactate, acetoacetate and unsaturated lipids in serum from metformin treated patients compared to untreated ones. UPLC/MS in positive electrospray ionization detected increased tryptophan and decreased lysophosphatidylcholines (C16:0 LPC, C18:0 LPC and C18:2 LPC) as well as phenylalanine in treated group. Both analytical techniques used in this study were able to detect biochemical changes in the serum of type 2 diabetes mellitus patients after the treatment of metformin hydrochloride, which may be helpful to the understanding of action mechanism of metformin hydrochloride.

An integrated metabonomic method for profiling of metabolic changes in carbon tetrachloride induced rat urine

Carbon tetrachloride (CCl(4)) is a well-known model compound for inducing chemical hepatic injury. This work characterizes the metabolism disorders of hepatotoxicity induced by CCl(4) in a Wistar rat model with a single dosage of 1 ml/kg. A seven-day long continuous collection of urine was performed in male rats in this experiment. Blood biochemistry and histopathology were examined to identify specific changes of liver hepatotoxicity. At the same time, an integrated analytical approach based on liquid chromatography coupled with mass spectrometry (LC-MS) was developed to map the metabolic response in urine. The current metabonomic approach based on LC-MS indicated 23 endogenous metabolites as biomarkers in urine associated with the hepatotoxicity induced by CCl(4). The underlying regulations of CCl(4)-perturbed metabolic pathways were discussed according to the identified metabolites. The present study proves the great potential of LC-MS based metabonomics in mapping metabolic response for toxicology.

Metabolomics and its application for non-invasive embryo assessment in IVF

Morphology and cleavage rate remain the mainstay of embryo assessment. However, a number of additional technologies for this application are under investigation. These include the measurement of glucose, lactate, pyruvate or amino acid levels in the embryo culture media, assessment of oxygen consumption by the embryo, genomic and proteomic profiling, and most recently, analytical examination of the embryonic metabolome. As the number of assisted reproduction cycles increases worldwide, improvements in the ability to quickly and non-invasively identify the best embryos for transfer remain a critical goal for reproductive medicine. Recent studies suggest that metabolomic profiling of embryo culture media using optical and non-optical spectroscopies may provide a useful adjunct to the current embryo assessment strategies and provide insight into the phenotype of embryos with increasing reproductive potential.