Metabolomic profiling using Orbitrap Fourier transform mass spectrometry with hydrophilic interaction chromatography: a method with wide applicability to analysis of biomolecules

Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining

Metabolomics experiments seldom achieve their aim of comprehensively covering the entire metabolome. However, important information can be gleaned even from sparse datasets, which can be facilitated by placing the results within the context of known metabolic networks. Here we present a method that allows the automatic assignment of identified metabolites to positions within known metabolic networks, and, furthermore, allows automated extraction of sub-networks of biological significance. This latter feature is possible by use of a gap-filling algorithm. The utility of the algorithm in reconstructing and mining of metabolomics data is shown on two independent datasets generated with LC-MS LTQ-Orbitrap mass spectrometry. Biologically relevant metabolic sub-networks were extracted from both datasets. Moreover, a number of metabolites, whose presence eluded automatic selection within mass spectra, could be identified retrospectively by virtue of their inferred presence through gap filling. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-009-0196-9) contains supplementary material, which is available to authorized users.

The evolution of metabolic profiling in parasitology

The uses of metabolic profiling technologies such as mass spectrometry and nuclear magnetic resonance spectroscopy in parasitology have been multi-faceted. Traditional uses of spectroscopic platforms focused on determining the chemical composition of drugs or natural products used for treatment of parasitic infection. A natural progression of the use of these tools led to the generation of chemical profiles of the parasite in in vitro systems, monitoring the response of the parasite to chemotherapeutics, profiling metabolic consequences in the host organism and to deriving host-parasite interactions. With the dawn of the post-genomic era the paradigm in many research areas shifted towards Systems Biology and the integration of biomolecular interactions at the level of the gene, protein and metabolite. Although these technologies have yet to deliver their full potential, metabolic profiling has a key role to play in defining diagnostic or even prognostic metabolic signatures of parasitic infection and in deciphering the molecular mechanisms underpinning the development of parasite-induced pathologies. The strengths and weaknesses of the various spectroscopic technologies and analytical strategies are summarized here with respect to achieving these goals.

Coupling liquid chromatography to Orbitrap mass spectrometry

The Orbitrap mass analyzer has become a mainstream mass spectrometry technique. In addition to providing a brief introduction to the Orbitrap technology and its continuing development, this article reviews the most recent publications quoting the use of the Orbitrap detection for a variety of chromatographic separation techniques. Its coupling to reversed-phase liquid chromatography (LC) represents undoubtedly the most ubiquitous approach to both small molecule and proteomic analyses. Multi-dimensional LC separations have an important role to play in the proteomics applications while an ultra-high-pressure LC is more frequently encountered in the area of metabolomics and metabolite analysis. Recently, special chromatographic techniques such as hydrophilic interaction chromatography and its variations have also been also cited with the Orbitrap detection.

Eating at the table of another: metabolomics of host-parasite interactions

The application of metabolomics, the global analysis of metabolite levels, to the study of protozoan parasites has become an important tool for understanding the host-parasite relationship and holds promise for the development of direly needed therapeutics and improved diagnostics. Research advances over the past decade have opened the door for a systems biology approach to protozoan parasites with metabolomics, providing a crucial readout of metabolic activity. In this review, we highlight recent metabolomic approaches to protozoan parasites, including metabolite profiling, integration with genomics, transcription, and proteomic analysis, and the use of metabolic fingerprints for the diagnosis of parasitic infections.

Metabolomic systems biology of trypanosomes

Metabolomics analysis, which aims at the systematic identification and quantification of all metabolites in biological systems, is emerging as a powerful new tool to identify biomarkers of disease, report on cellular responses to environmental perturbation, and to identify the targets of drugs. Here we discuss recent developments in metabolomic analysis, from the perspective of trypanosome research, highlighting remaining challenges and the most promising areas for future research.

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.

The potential of mass spectrometry for the global profiling of parasite metabolomes

The strengths and limitations of existing mass spectrometry methods for metabolite detection and identification are discussed. A brief review is made of the methods available for quenching and extraction of cells or organisms prior to instrumental analysis. The techniques available for carrying out mass spectrometry-based profiling of metabolomes are discussed using the analysis of extracts from trypanosomes to illustrate various points regarding methods of separation and mass spectrometric analysis. The advantages of hydrophilic interaction chromatography (HILIC) for the analysis of polar metabolites are discussed. The challenges of data processing are outlined and illustrated using the example of ThermoFisher's Sieve software. The existing literature on applications of mass spectrometry to the profiling of parasite metabolomes is reviewed.

Chromatographic and mass spectrometric analysis of glutathione in biological samples

Biological thiol compounds are classified into high-molecular-mass protein thiols and low-molecular-mass free thiols. Endogenous low-molecular-mass thiol compounds, namely, reduced glutathione (GSH) and its corresponding disulfide, glutathione disulfide (GSSG), are very important molecules that participate in a variety of physiological and pathological processes. GSH plays an essential role in protecting cells from oxidative and nitrosative stress and GSSG can be converted into the reduced form by action of glutathione reductase. Measurement of GSH and GSSG is a useful indicator of oxidative stress and disease risk. Many publications have reported successful determination of GSH and GSSG in biological samples. In this article, we review newly developed techniques, such as liquid chromatography coupled with mass spectrometry and tandem mass spectrometry, for identifying GSH bound to proteins, or for localizing GSH in bound or free forms at specific sites in organs and in cellular locations.

Kynurenine pathway inhibition reduces central nervous system inflammation in a model of human African trypanosomiasis

Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasites Trypanosoma brucei rhodesiense or Trypanosoma brucei gambiense, and is a major cause of systemic and neurological disability throughout sub-Saharan Africa. Following early-stage disease, the trypanosomes cross the blood-brain barrier to invade the central nervous system leading to the encephalitic, or late stage, infection. Treatment of human African trypanosomiasis currently relies on a limited number of highly toxic drugs, but untreated, is invariably fatal. Melarsoprol, a trivalent arsenical, is the only drug that can be used to cure both forms of the infection once the central nervous system has become involved, but unfortunately, this drug induces an extremely severe post-treatment reactive encephalopathy (PTRE) in up to 10% of treated patients, half of whom die from this complication. Since it is unlikely that any new and less toxic drug will be developed for treatment of human African trypanosomiasis in the near future, increasing attention is now being focussed on the potential use of existing compounds, either alone or in combination chemotherapy, for improved efficacy and safety. The kynurenine pathway is the major pathway in the metabolism of tryptophan. A number of the catabolites produced along this pathway show neurotoxic or neuroprotective activities, and their role in the generation of central nervous system inflammation is well documented. In the current study, Ro-61-8048, a high affinity kynurenine-3-monooxygenase inhibitor, was used to determine the effect of manipulating the kynurenine pathway in a highly reproducible mouse model of human African trypanosomiasis. It was found that Ro-61-8048 treatment had no significant effect (P = 0.4445) on the severity of the neuroinflammatory pathology in mice during the early central nervous system stage of the disease when only a low level of inflammation was present. However, a significant (P = 0.0284) reduction in the severity of the neuroinflammatory response was detected when the inhibitor was administered in animals exhibiting the more severe, late central nervous system stage, of the infection. In vitro assays showed that Ro-61-8048 had no direct effect on trypanosome proliferation suggesting that the anti-inflammatory action is due to a direct effect of the inhibitor on the host cells and not a secondary response to parasite destruction. These findings demonstrate that kynurenine pathway catabolites are involved in the generation of the more severe inflammatory reaction associated with the late central nervous system stages of the disease and suggest that Ro-61-8048 or a similar drug may prove to be beneficial in preventing or ameliorating the PTRE when administered as an adjunct to conventional trypanocidal chemotherapy.

Metabolomics: moving to the clinic

Assessment of a biological system by means of global and non-targeted metabolite profiling--metabolomics or metabonomics--provides the investigator with molecular information that is close to the phenotype in question in the sense that metabolites are an ultimate product of gene, mRNA, and protein activity. Over the last few years, there has been a rapidly growing number of metabolomics applications aimed at finding biomarkers which could assist diagnosis, provide therapy guidance, and evaluate response to therapy for particular diseases. Also, within the fields of drug discovery, drug toxicology, and personalized pharmacology, metabolomics is emerging as a powerful tool. This review seeks to update the reader on analytical strategies, biomarker findings, and implications of metabolomics for the clinic. Particular attention is paid to recent biomarkers found related to neurological, cardiovascular, and cancer diseases. Moreover, the impact of metabolomics in the drug discovery and development process is examined.

Quantitative profiling of polar cationic metabolites in human cerebrospinal fluid by reversed-phase nanoliquid chromatography/mass spectrometry

Reversed-phase (RP) nanoliquid chromatography (LC)/mass spectrometry (MS) is widely used for proteome analysis, but hydrophilic metabolites are poorly retained on RP columns. We describe here the development and application of an efficient, robust, and quantitative nano-LC/MS method for cationic metabolome analysis in the positive ionization mode without any derivatization of analytes. Various stationary phases for nano-LC, coating of the internal wall of the capillary column, and various mobile phases were evaluated in terms of separation and peak shapes for 33 hydrophilic metabolites, including nonderivatized amino acids. Polar cationic compounds were strongly bound to mixed-functional RP with cation exchange mode resin, and the best separation was obtained with hydrophilic internal wall coating and a two-step trifluoroacetic acid (TFA) gradient in methanol as the mobile phase. Simple, but optimized, sample processing and the use of a high content of methanol allowed robust nano-LC/MS analysis. Our developed method was applied for biomarker discovery in Alzheimer's disease (AD). Several hundred peaks were detected from 10 microL of cerebrospinal fluid (CSF). In a principal component analysis (PCA) plot using peak intensities without normalization, peak separation depended on the experimental date, not disease state. Therefore, constant amounts of two stable isotope-labeled amino acids, Val and Lys, were added as internal standards (ISs) to each sample before processing. These ISs were eluted in different gradient slopes in the two-step gradient, and the normalized peak ratios using the corresponding ISs gave a unique group of PCA scores which could distinguish AD CSF samples from age-matched control CSF samples.

Identification and characterization of active compounds and their metabolites by high-performance liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry after oral administration of a herbal extract of Epimedium koreanum Nakai to rats

Epimedium is an important traditional Chinese medicine that is widely used throughout China as a tonic, aphrodisiac, and antirheumatic medicine. Flavonoids are considered to be the active compounds in Epimedium. In the study reported here, high-performance liquid chromatography coupled with Fourier transform-ion cyclotron resonance mass spectrometry (HPLC/FTICR-MS) was developed to identify active compounds and their metabolites after oral administration of a herbal extract of Epimedium koreanum Nakai to rats, using parent mass list triggered data-dependent multiple-stage accurate mass analysis at a resolving power of 100 000 in the external calibration mode. Nine flavonoids were identified in rats. The chemical formulae with unsaturation numbers calculated from accurate m/z values of precursor and product ions were used to assign the structures of metabolites and the chemical sites of metabolism. The mass accuracies obtained for all full-scan MS and MS(n) spectra were within 3 ppm (<1 ppm in most cases). The majority of the metabolites identified have been previously reported, but three compounds were noted for the first time in rats. By contrasting the analytical results obtained from the herbal extract with those obtained from biological specimens, the profile of flavonoid biotransformation in Epimedium was obtained and the metabolic pathways of these components, in rats, are described. The results should be of use in targeting potential active ingredients in Epimedium.

Metabolomic profiling of Drosophila using liquid chromatography Fourier transform mass spectrometry

Hydrophilic interaction chromatography (HILIC) interfaced with an Orbitrap Fourier transform mass spectrometer (FT-MS) was used to carry out metabolomic profiling of the classical Drosophila mutation, rosy (ry). This gene encodes a xanthine oxidase/dehydrogenase. In addition to validating the technology by detecting the same changes in xanthine, hypoxanthine, urate and allantoin that have been reported classically, completely unsuspected changes were detected in each of the tryptophan, arginine, pyrimidine and glycerophospholipid metabolism pathways. The rosy mutation thus ramifies far more widely than previously detected.

Liquid chromatography-mass spectrometry in metabolite profiling

Recent advances in the use of liquid chromatography-mass spectrometry for the study of metabolomics are reviewed. Sample preparations of biofluids and practical aspects of ultra-high pressure liquid chromatography are discussed. Applicability of different kinds of mass spectrometers for metabolite profiling is described. New tools-ion mobility spectroscopy and automated chip-based nanoelectrospray system with potentials to be applied in the metabolomics analysis are described.