Helen G. Gika

Liquid chromatography–mass spectrometry based global metabolite profiling: A review

Untargeted, global metabolite profiling (often described as metabonomics or metabolomics) represents an expanding research topic and is, potentially, a major pillar for systems biology studies. To obtain holistic metabolic profiles from complex samples, such as biological fluids or tissue extracts, requires powerful, high resolution and information-rich analytical methods and for this spectroscopic technologies are generally used. Mass spectrometry, coupled to liquid chromatography (LC-MS), is increasingly being used for such investigations as a result of the significant advances in both technologies over the past decade. Here we try to critically review the topic of LC-MS-based global metabolic profiling and describe and compare the results offered by different analytical strategies and technologies. This review highlights the current challenges, limitations and opportunities of the current methodology.

Current practice of liquid chromatography-mass spectrometry in metabolomics and metabonomics.

Based on publication and citation numbers liquid chromatography (LC-MS) has become the major analytical technology in the field of global metabolite profiling. This dominance reflects significant investments from both the research community and instrument manufacturers. Here an overview of the approaches taken for LC-MS-based metabolomics research is given, describing critical steps in the realisation of such studies: study design and its needs, specific technological problems to be addressed and major obstacles in data treatment and biomarker identification. The current state of the art for LC-MS-based analysis in metabonomics/metabolomics is described including recent developments in liquid chromatography, mass spectrometry and data treatment as these are applied in metabolomics underlining the challenges, limitations and prospects for metabolomics research. Examples of the application of metabolite profiling in the life sciences focusing on disease biomarker discovery are highlighted. In addition, new developments and future prospects are described.

Evaluation of the repeatability of ultra-performance liquid chromatography–TOF-MS for global metabolic profiling of human urine samples ☆

The application of reversed-phase ultra-performance liquid chromatography, based on the use of sub 2 microm particles, combined with time-of-flight mass spectrometry has been investigated for the production of global metabolite profiles from human urine. The stability and repeatability of the methodology, which employed gradient elution, was determined by the repeat analysis of a pooled quality control (QC) sample. As seen in previous studies conducted with conventional LC-MS an element of system conditioning was required to obtain reproducible data, as the initial injections were unrepresentative. However, once the system had equilibrated excellent repeatability in terms of retention time, signal intensity and mass accuracy was seen providing confidence that for this matrix, the within-day repeatability of UPLC-TOF-MS was sufficient to assure data quality in global metabolic profiling applications.

Hydrophilic interaction chromatography coupled to MS for metabonomic/metabolomic studies

Hydrophilic interaction chromatography (HILIC) is a relatively recently introduced mode of liquid-phase separations. Recently, HILIC has been used for coupling to MS in metabonomic/metabolomic studies to provide a complementary tool to the widely used reversed-phase (RP) chromatographic separations. The combination of HILIC with MS detection covers a number of polar metabolites that are typically nonretained in RPLC-mode separations and thus enlarging the number of detected analytes. This way of metabolite profiling thus provides more comprehensive metabolome coverage than using RP chromatography alone. This review describes the applications and the utility of HILIC-MS in metabolomic/metabonomic studies and highlights certain characteristic examples in the life and plant-food sciences.

Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice

Background The gastrointestinal tract microbiota (GTM) of mammals is a complex microbial consortium, the composition and activities of which influences mucosal development, immunity, nutrition and drug metabolism. It remains unclear whether the composition of the dominant GTM is conserved within animals of the same strain and whether stable GTMs are selected for by host-specific factors or dictated by environmental variables. Methodology/Principal Findings The GTM composition of six highly inbred, genetically distinct strains of mouse (C3H, C57, GFEC, CD1, CBA nu/nu and SCID) was profiled using eubacterial –specific PCR-DGGE and quantitative PCR of feces. Animals exhibited strain-specific fecal eubacterial profiles that were highly stable (c. >95% concordance over 26 months for C57). Analyses of mice that had been relocated before and after maturity indicated marked, reproducible changes in fecal consortia and that occurred only in young animals. Implantation of a female BDF1 mouse with genetically distinct (C57 and Agoutie) embryos produced highly similar GTM profiles (c. 95% concordance) between mother and offspring, regardless of offspring strain, which was also reflected in urinary metabolite profiles. Marked institution-specific GTM profiles were apparent in C3H mice raised in two different research institutions. Conclusion/Significance Strain-specific data were suggestive of genetic determination of the composition and activities of intestinal symbiotic consortia. However, relocation studies and uterine implantation demonstrated the dominance of environmental influences on the GTM. This was manifested in large variations between isogenic adult mice reared in different research institutions.

Hydrophilic interaction and reversed-phase ultra-performance liquid chromatography TOF-MS for metabonomic analysis of Zucker rat urine.

Hydrophilic interaction chromatography (HILIC) provides a complementary technique to RP methods for the retention of polar analytes for LC-MS-based metabonomic studies. Combining the advantages of both RP and HILIC separations with the efficient and rapid separations obtained using sub-2 mum particles via the recently introduced ultra-performance LC (UPLC) enables increased coverage of the metabolites present in biological samples to be achieved. Here an HILIC-UPLC-MS method was developed to provide metabolite profiles for urine samples obtained from male Zucker rats. The resulting data were compared with results obtained for the same samples by RP-UPLC-MS and demonstrated the complementary nature of the two separations with both methods enabling discrimination between the different sample types. Interestingly sample type differentiation was based on different markers.

Quantitative profiling of polar primary metabolites using hydrophilic interaction ultrahigh performance liquid chromatography-tandem mass spectrometry

A hydrophilic interaction liquid chromatography (HILIC)-MS/MS profiling method was developed for the efficient separation and quantification of small polar molecules, mostly primary metabolites. The method was based on an ultrahigh performance liquid chromatography (UHPLC) separation system coupled with ESI mass spectrometry on a triple quadrupole mass spectrometer, operating in both positive and negative ionisation mode using rapid polarity switching. With the developed method quantitation of 135 compounds belonging in four major classes of polar compounds (sugars, aminoacids, organic acids and amines) was achieved in a single run of 30 min. The method was applied to grape extracts from different varieties and provided information on primary metabolite content. Multivariate statistical analysis was applied using the concentrations found, with the aim of investigating the differences in metabolite profiles. Classification of grapes according to their skin colour was carried out using principle component analysis based on the concentration variation of a number of the metabolites studied.

(1)H NMR-based metabonomic investigation of the effect of two different exercise sessions on the metabolic fingerprint of human urine.

Physical exercise modifies animal metabolism profoundly. Until recently, biochemical investigations related to exercise focused on a small number of biomolecules. In the present study, we used a holistic analytical approach to investigate changes in the human urine metabolome elicited by two exercise sessions differing in the duration of the rest interval between repeated efforts. Twelve men performed three sets of two 80 m maximal runs separated by either 10 s or 1 min of rest. Analysis of pre- and postexercise urine samples by (1)H NMR spectroscopy and subsequent multivariate statistical analysis revealed alterations in the levels of 22 metabolites. Urine samples were safely classified according to exercise protocol even when applying unsupervised methods of statistical analysis. Separation of pre- from postexercise samples was mainly due to lactate, pyruvate, hypoxanthine, compounds of the Krebs cycle, amino acids, and products of branched-chain amino acid (BCAA) catabolism. Separation of the two rest intervals was mainly due to lactate, pyruvate, alanine, compounds of the Krebs cycle, and 2-oxoacids of BCAA, all of which increased more with the shorter interval. Metabonomics provides a powerful methodology to gain insight in metabolic changes induced by specific training protocols and may thus advance our knowledge of exercise biochemistry.

LC-MS based global metabolite profiling of grapes: solvent extraction protocol optimisation

Optimal solvent conditions for grape sample preparation were investigated for the purpose of metabolite profiling studies, with the aim of obtaining as many features as possible with the best analytical repeatability. Mixtures of water, methanol and chloroform in different combinations were studied as solvents for the extraction of ground grapes. The experimental design used a two stage study to find the optimum extraction medium. The extracts obtained were further purified using solid phase extraction and analysed using a UPLC full scan TOF MS with both reversed phase and hydrophilic interaction chromatography. The data obtained were processed using data extraction algorithms and advanced statistical software for data mining. The results obtained indicated that a fairly broad optimal area for solvent composition could be identified, containing approximately equal amounts of methanol and chloroform and up to 20% water. Since the water content of the samples was variable, the robustness of the optimal conditions suggests these are appropriate for large scale profiling studies for characterisation of the grape metabolome.

Metabolite profiling on apple volatile content based on solid phase microextraction and gas-chromatography time of flight mass spectrometry.

A headspace SPME GC-TOF-MS method was developed for the acquisition of metabolite profiles of apple volatiles. As a first step, an experimental design was applied to find out the most appropriate conditions for the extraction of apple volatile compounds by SPME. The selected SPME method was applied in profiling of four different apple varieties by GC-EI-TOF-MS. Full scan GC-MS data were processed by MarkerLynx software for peak picking, normalisation, alignment and feature extraction. Advanced chemometric/statistical techniques (PCA and PLS-DA) were used to explore data and extract useful information. Characteristic markers of each variety were successively identified using the NIST library thus providing useful information for variety classification. The developed HS-SPME sampling method is fully automated and proved useful in obtaining the fingerprint of the volatile content of the fruit. The described analytical protocol can aid in further studies of the apple metabolome.