CE‐MS for metabolomics: Developments and applications in the period 2016–2018

In the field of metabolomics, CE‐MS is now recognized as a strong analytical technique for the analysis of (highly) polar and charged metabolites in a wide range of biological samples. Over the past few years, significant attention has been paid to the design and improvement of CE‐MS approaches for (large‐scale) metabolic profiling studies and for establishing protocols in order to further expand the role of CE‐MS in metabolomics. In this paper, which is a follow‐up of a previous review paper covering the years 2014–2016 (Electrophoresis 2017, 38, 190–202), main advances in CE‐MS approaches for metabolomics studies are outlined covering the literature from July 2016 to June 2018. Aspects like developments in interfacing designs and data analysis tools for improving the performance of CE‐MS for metabolomics are discussed. Representative examples highlight the utility of CE‐MS in the fields of biomedical, clinical, microbial, and plant metabolomics. A complete overview of recent CE‐MS‐based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings and MS detection mode. Finally, some general conclusions and perspectives are given.     

CE–MS for anionic metabolic profiling: An overview of methodological developments

The efficient profiling of highly polar and charged metabolites in biological samples remains a huge analytical challenge in metabolomics. Over the last decade, new analytical techniques have been developed for the selective and sensitive analysis of polar ionogenic compounds in various matrices. Still, the analysis of such compounds, notably for acidic ionogenic metabolites, remains a challenging endeavor, even more when the available sample size becomes an issue for the total analytical workflow. In this paper, we give an overview of the possibilities of capillary electrophoresis‐mass spectrometry (CE–MS) for anionic metabolic profiling by focusing on main methodological developments. Attention is paid to the development of improved separation conditions and new interfacing designs in CE–MS for anionic metabolic profiling. A complete overview of all CE–MS‐based methods developed for this purpose is provided in table format (Table 1) which includes information on sample type, separation conditions, mass analyzer and limits of detection (LODs). Selected applications are discussed to show the utility of CE–MS for anionic metabolic profiling, especially for small‐volume biological samples. On the basis of the examination of the reported literature in this specific field, we conclude that there is still room for the design of a highly sensitive and reliable CE–MS method for anionic metabolic profiling. A rigorous validation and the availability of standard operating procedures would be highly favorable in order to make CE–MS an alternative, viable analytical technique for metabolomics.     

Metabolic profiling for the identification of Huntington biomarkers by on‐line solid‐phase extraction capillary electrophoresis mass spectrometry combined with advanced data analysis tools

In this work, an untargeted metabolomic approach based on sensitive analysis by on‐line solid‐phase extraction capillary electrophoresis mass spectrometry (SPE‐CE‐MS) in combination with multivariate data analysis is proposed as an efficient method for the identification of biomarkers of Huntington's disease (HD) progression in plasma. For this purpose, plasma samples from wild‐type (wt) and HD (R6/1) mice of different ages (8, 12, and 30 weeks), were analyzed by C₁₈‐SPE‐CE‐MS in order to obtain the characteristic electrophoretic profiles of low molecular mass compounds. Then, multivariate curve resolution alternating least squares (MCR‐ALS) was applied to the multiple full scan MS datasets. This strategy permitted the resolution of a large number of metabolites being characterized by their electrophoretic peaks and their corresponding mass spectra. A total number of 29 compounds were relevant to discriminate between wt and HD plasma samples, as well as to follow‐up the HD progression. The intracellular signaling was found to be the most affected metabolic pathway in HD mice after 12 weeks of birth, when mice already showed motor coordination deficiencies and cognitive decline. This fact agreed with the atrophy and dysfunction of specific neurons, loss of several types of receptors, and changed expression of neurotransmitters.     

Proteomics comparison of exosomes from serum and plasma between ultracentrifugation and polymer‐based precipitation kit methods

Exosomes are vesicles with sizes ranging from 30 to 150 nm. The analysis and detection of blood exosomes offers an effective route for cancer diagnosis, prognosis assessment, and therapeutic evaluation of diseases. Due to the difference in separation procedure, collection method and the usage of anticoagulants, serum and plasma samples show diversity test results. In order to evaluate the isolation effect of exosomes in serum and plasma samples, two commonly used exosomal isolation methods, ultracentrifugation and polymer‐based precipitation kit, were used, respectively. And the isolation effects were evaluated by comparing the composition and abundant of proteins from isolated exosomes based on MS‐based proteomics analysis. The results showed that the plasma exosomes extracted by ultracentrifugation identified more exosome biomarkers, and the concentrations of these biomarkers were higher than others. And plasma exosomes could be a better sample for blood‐based proteomics research of exosomes. It would be more useful for future targeted biomarker discovery.     

Study of immobilized metal affinity chromatography sorbents for the analysis of peptides by on‐line solid‐phase extraction capillary electrophoresis‐mass spectrometry

Several commercial immobilized metal affinity chromatography sorbents were evaluated in this study for the analysis of two small peptide fragments of the amyloid β‐protein (Aβ) (Aβ(1–15) and Aβ(10–20) peptides) by on‐line immobilized metal affinity SPE‐CE (IMA‐SPE‐CE). The performance of a nickel metal ion (Ni(II)) sorbent based on nitrilotriacetic acid as a chelating agent was significantly better than two copper metal ion (Cu(II)) sorbents based on iminodiacetic acid. A BGE of 25 mM phosphate (pH 7.4) and an eluent of 50 mM imidazole (in BGE) yielded a 25‐fold and 5‐fold decrease in the LODs by IMA‐SPE‐CE‐UV for Aβ(1–15) and Aβ(10–20) peptides (0.1 and 0.5 μg/mL, respectively) with regard to CE‐UV (2.5 μg/mL for both peptides). The phosphate BGE was also used in IMA‐SPE‐CE‐MS, but the eluent needed to be substituted by a 0.5% HAc v/v solution. Under optimum preconcentration and detection conditions, reproducibility of peak areas and migration times was acceptable (23.2 and 12.0%RSD, respectively). The method was more sensitive for Aβ(10–20) peptide, which could be detected until 0.25 μg/mL. Linearity for Aβ(10–20) peptide was good in a narrow concentration range (0.25–2.5 μg/mL, R² = 0.93). Lastly, the potential of the optimized Ni(II)‐IMA‐SPE‐CE‐MS method for the analysis of amyloid peptides in biological fluids was evaluated by analyzing spiked plasma and serum samples.     

Characterization and tentative identification of new flunitrazepam metabolites in authentic human urine specimens using liquid chromatography‐Q exactive‐HF hybrid quadrupole‐Orbitrap‐mass spectrometry (LC‐QE‐HF‐MS)

Flunitrazepam (FNZ) is a potent hypnotic, sedative, and amnestic drug used to treat severe insomnia. In our recent study, FNZ metabolic profiles were investigated carefully. Six authentic human urine samples were purified using solid phase extraction (SPE) without enzymatic hydrolysis, and urine extracts were then analyzed by liquid chromatography‐Q exactive‐HF hybrid quadrupole‐Orbitrap‐mass spectrometry (LC‐QE‐HF‐MS), using the full scan positive ion mode and targeted MS/MS (ddms2) technique to make accurate mass measurements. There were 25 metabolites, including 13 phase I and 12 phase II metabolites, which were detected and tentatively identified by LC‐QE‐HF‐MS. In addition, nine previously unreported phase II glucuronide conjugates and four phase I metabolites are reported here for the first time. Eight metabolic pathways, including N‐reduction and O‐reduction, N‐glucuronidation, O‐glucuronidation, mono‐hydroxylation and di‐hydroxylation, demethylation, acetylation, and combinations, were implicated in this work, and 2‐O‐reduction together with dihydroxylation were two novel metabolic pathways for FNZ that were identified tentatively. Although 7‐amino FNZ is widely considered to be the primary metabolite, a previously unreported metabolites (M12) can also serve as a potential biomarker for FNZ misuse.     

Use of stable isotope labeled probes to facilitate liquid chromatography/mass spectrometry based high‐throughput screening of time‐dependent CYP inhibitors

Inhibition curve shift is a commonly used approach for screening of time‐dependent CYP inhibitors which requires parallel paired incubations to obtain two inhibition curves for comparison. For the control incubation, a test compound is co‐incubated with a probe substrate in human liver microsomes (HLM) fortified with NADPH; for the time‐dependent incubation (TDI), the test compound is pre‐incubated with NADPH‐fortified HLM followed by a secondary incubation with a probe substrate. For both incubations, enzyme activity is measured respectively by liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis of the CYP‐specific metabolite, and a TDI inhibitor can be readily identified by inhibition curve shifting as a result of CYP inactivation by the test compound during the pre‐incubation. In the present study, we describe an alternative approach to facilitate TDI screening in which stable isotope labeled CYP‐specific probes are used for the TDI, and non‐labeled substrates are included in the control incubation. Because CYP‐specific metabolites produced in the TDI are stable isotope labeled, two sets of incubation samples can be combined and then simultaneously analyzed by LC/MS/MS in the same batch run to reduce the run time. This new method has been extensively validated using both a number of known competitive and TDI inhibitors specific to five most common CYPs such as 1A2, 2C9, 2C19, 2D6, and 3A4. The assay is performed in a 96‐well format and can be fully automated. Compared to the traditional method, this approach in combination with sample pooling and a short LC/MS/MS gradient significantly enhances the throughput of TDI screening and thus can be easily implemented in drug discovery to evaluate a large number of compounds without adding additional resource. Copyright © 2010 John Wiley & Sons, Ltd.     

A benchmark spike‐in data set for biomarker identification in metabolomics

The development and the validation of innovative approaches for biomarker selection are of paramount importance in many ‐omics technologies. Unfortunately, the actual testing of new methods on real data is difficult, because in real data sets, one can never be sure about the “true” biomarkers. In this paper, we present a publicly available metabolomic ultra performance liquid chromatography–mass spectrometry spike‐in data set for apples. The data set consists of 10 control samples and three spiked sets of the same size, where naturally occurring compounds are added in different concentrations. In this sense, the data set can serve as a test bed to assess the performance of new algorithms and compare them with previously published results. We illustrate some of the possibilities provided by this spike‐in data set by comparing the performance of two popular biomarker‐selection methods, the univariate t‐test and the multivariate variable importance in projection. To promote a widespread use of the data, raw data files as well as preprocessed peak lists are made available. Copyright © 2012 John Wiley & Sons, Ltd.     

Critical evaluation of screening techniques for emerging environmental contaminants based on accurate mass measurements with time‐of‐flight mass spectrometry

Emerging contaminants from wastewater effluent samples were analysed, using posttarget and nontarget analysis techniques. The samples were analysed with an ultra performance liquid chromatograph‐time‐of‐flight mass spectrometer (UPLC‐TOF‐MS), and the resulting data were processed with commercial deconvolution software. The method works well for posttarget analysis with prior information about the retention times of the compounds of interest. With positive polarity, 63 of 66 compounds and with negative polarity, 18 of 20 compounds were correctly identified in a spiked sample, while two compounds of a total of 88 fell out of the mass range. Furthermore, a four‐stage process for identification was developed for the posttarget analysis lacking the retention time data. In the process, the number of candidate compounds was reduced by using the accurate mass of selected compounds in two steps (stages 1 and 2), structure–property relationships (stage 3) and isotope patterns of the analytes (stage 4). The process developed was validated by analysing wastewater samples spiked with 88 compounds. This procedure can be used to gain a preliminary indication of the presence of certain analytes in the samples. Nontarget analysis was tested by applying a theoretical mass spectra library for a wastewater sample spiked with six pharmaceuticals. The results showed a high number of false identifications. In addition, manual processing of the data was considered laborious and ineffective. Finally, the posttarget analysis was applied to a real wastewater sample. The analysis revealed the presence of six compounds that were afterwards confirmed with standard compounds as being correct. Three psycholeptics (nordiazepam, oxazepam and temazepam) could be tentatively identified, using the identification process developed. Posttarget analysis with UPLC‐TOF‐MS proved to be a promising method for analysing wastewater samples, while we concluded that the software for nontarget analysis will need improvement before it can be used in environmental analytical work with LC‐TOF‐MS systems. Copyright © 2012 John Wiley & Sons, Ltd.     

13C‐Isotope Labeled Surrogate for Estimating Organophosphorus Pesticides in Agricultural Products by Gas Chromatography‐Mass Spectrometry

¹³C‐isotope labeled paraoxon‐ethyl (¹³C₂‐EP) and deuterium‐labeled paraoxon‐methyl (D₆‐MP) were synthesized and employed as the surrogate (SS) and the internal standard (IS) in organophosphorus pesticides (OPs) spiking agricultural QC samples. The residual amounts of OPs were determined with gas chromatography‐mass spectrometry (GC‐MS) method. The isotope‐labeled compounds used in this study could assist the analysts to estimate the appropriateness and the uncertainties produced by pre‐treatment process. It was found that these isotope labeled compounds could improve the accuracy (10% to 40% of quantitative analysis), and provide efficacious calibration for the spiking recoveries of OPs in some agricultural samples.     

High‐throughput determination of Sudan Azo‐dyes within powdered chili pepper by paper spray mass spectrometry

A high‐throughput mass spectrometric method is presented for the simultaneous detection of Sudan I, II, III, IV and Para‐Red azo‐dyes in foodstuff. The method is based on the use of paper spray mass spectrometry (MS) and deuterium‐labeled internal standards on a triple‐quadrupole instrument. A detailed assay of each azo‐dye was performed by the isotope dilution method, through the precursor ion scan approach, using deuterium‐labeled internal standards. The gas‐phase breakdown pattern of each labeled and unlabeled analogue displays the naphthoic moiety as a common fragment. Sudan dyes can be determined above the threshold of 1 ppm. Paper spray allows for a wide range of analytes and samples to be investigated by MS in the open air and without sample preparation and bypassing chromatography. Copyright © 2013 John Wiley & Sons, Ltd.     

A 2‐D‐HPLC‐CE platform coupled to ESI‐TOF‐MS to characterize the phenolic fraction in olive oil

A 2‐D‐HPLC/CE method was developed to separate and characterize more in depth the phenolic fraction of olive oil samples. The method involves the use of semi‐preparative HPLC (C18 column 250×10 mm, 5 μm) as a first dimension of separation to isolate phenolic fractions from commercial extra‐virgin olive oils and CE coupled to TOF‐MS (CE‐TOF‐MS) as a second dimension, to analyze the composition of the isolated fractions. Using this method, a large number of compounds were tentatively identified, some of them by first time, based on the information concerning high mass accuracy and the isotopic pattern provided by TOF‐MS analyzer together with the chemical knowledge and the behavior of the compounds in HPLC and CE. From these results it can be concluded that 2‐D‐HPLC‐CE‐MS provides enough resolving power to separate hundreds of compounds from highly complex samples, such as olive oil. Furthermore, in this paper, the isolated phenolic fractions have been used for two specific applications: quantification of some components of extra‐virgin olive oil samples in terms of pure fractions, and in vitro studies of its anti‐carcinogenic capacity.     

NMR‐based metabolomics coupled with pattern recognition methods in biomarker discovery and disease diagnosis

Molecular biomarkers could detect biochemical changes associated with disease processes. The key metabolites have become an important part for improving the diagnosis, prognosis, and therapy of diseases. Because of the chemical diversity and dynamic concentration range, the analysis of metabolites remains a challenge. Assessment of fluctuations on the levels of endogenous metabolites by advanced NMR spectroscopy technique combined with multivariate statistics, the so‐called metabolomics approach, has proved to be exquisitely valuable in human disease diagnosis. Because of its ability to detect a large number of metabolites in intact biological samples with isotope labeling of metabolites using nuclei such as H, C, N, and P, NMR has emerged as one of the most powerful analytical techniques in metabolomics and has dramatically improved the ability to identify low concentration metabolites and trace important metabolic pathways. Multivariate statistical methods or pattern recognition programs have been developed to handle the acquired data and to search for the discriminating features from biosample sets. Furthermore, the combination of NMR with pattern recognition methods has proven highly effective at identifying unknown metabolites that correlate with changes in genotype or phenotype. The research and clinical results achieved through NMR investigations during the first 13 years of the 21st century illustrate areas where this technology can be best translated into clinical practice. In this review, we will present several special examples of a successful application of NMR for biomarker discovery, implications for disease diagnosis, prognosis, and therapy evaluation, and discuss possible future improvements. Copyright © 2013 John Wiley & Sons, Ltd.     

Absolute quantitation of host cell proteins in recombinant human monoclonal antibodies with an automated CZE‐ESI‐MS/MS system

We report the first use of CZE for absolute characterization of host cell proteins (HCPs) in recombinant human monoclonal antibodies. An electrokinetically pumped nanoelectrospray interface was used to couple CZE with a tandem mass spectrometer. Three isotopic‐labeled peptides (LSFDKDAMVAR, VDIVENQAMDTR, and LVSDEMVVELIEK) were synthesized by direct incorporation of an isotope‐labeled lysine or arginine. The heavy‐labeled peptides were spiked in the HCP digests at known concentrations. After CZE‐ESI‐MS/MS analysis, the peaks of native and isotopic‐labeled peptides were extracted with mass tolerance ≤ 5 ppm from the electropherograms, and the ratios of peak area between native and isotopic‐labeled peptides pairs were calculated. Calibration curves (the ratios of peak area versus spiked peptide amount) with R² values of 0.999, 0.997, and 0.999 were obtained for the three HCP peptides, and the absolute amounts of the three proteins present were determined to be at the picomole level in a 20 μg sample of digested HCPs. The target proteins were present at the 7–30 ppt level in the purified HCP samples.     

Searching for serum tumor markers for colorectal cancer using a 2‐D DIGE approach

Identification of specific protein markers for colorectal cancer (CRC) could provide a basis for its early diagnosis and detection, as well as clues to the molecular mechanisms governing cancer progression. In the present study, 2‐D DIGE coupled with MS was used to screen for biomarker candidates in the serum proteome of ten human CRC samples and ten healthy control samples. After pooling identical amounts of serum proteins (based on total protein concentration), albumin/IgG was depleted under partially denaturing conditions. Subsequently, the serum samples were labeled with three different CyDyes, and separated by 2‐D DIGE. After analysis with the biological variation analysis module of the DeCyder software, only three spots were found to be significantly elevated in all patient groups (with ratios from 1.52 to 9.08), whereas five spots were significantly down‐regulated in patients (with ratios from ?1.23 to ?10.21) (t‐test; p<0.05). Finally, two potential biomarkers, Transaldolase 1 and thyroid receptor interactor, were chosen for validation and analysis by ELISA with the serum of 30 CRC patients and 30 healthy controls. The serum levels of the two proteins correlated well with the 2‐D DIGE results. Thus, 2‐D DIGE approaches show great promise for biomarker discovery in CRC.     

Direct analysis of trace level bisphenol A,octylphenols and nonylphenol in bottled water and leached from bottles by ultra‐high‐performance liquid chromatography/tandem mass spectrometry

A high‐throughput method was developed for the direct analysis of trace level bisphenol A (BPA), 4‐n‐octylphenol (4‐n‐OP), 4‐tert‐octylphenol (4‐t‐OP) and 4‐n‐nonylphenol (4‐n‐NP) in water samples by ultra‐high‐performance liquid chromatography/tandem mass spectrometry (uHPLC/MS/MS) using an isotope‐labeled internal standard. Aliquots of water samples were spiked with the internal standard and analyzed without sample cleanup or enrichment. All target analytes were chromatographically separated within 3 min and detected using the highly selective multiple reaction monitoring (MRM) detection mode. The method detection limits were statistically calculated and ranged from 0.040 ppb (BPA) to 0.057 ppb (4‐n‐NP). Excellent correlation of determination was achieved for each analyte with r greater than 0.995. Precision was achieved within 8% relative standard deviation (RSD) for all analytes, and recoveries from spiked samples ranged from 97% to 106.2% except for 4‐n‐OP which may be corrected by using an isotope‐labeled analog as internal standard. This method was used for analyzing eight randomly selected bottled water samples and found no detectable target analytes. This method was also used to analyze target analytes leached from bottles (6 low cost bottles and 6 brand‐name baby‐feeding bottles). Low levels of BPA were found in three bottles after they had been heated in a microwave oven, and a trace amount of 4‐n‐NP was also found in three bottles. 4‐t‐OP, which has not been reported as a leachable chemical, was found in two brand name baby‐feeding bottles from the same manufacturer, and was confirmed with bottles from different batches. Copyright © 2010 John Wiley & Sons, Ltd.     

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 γ‐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 γ‐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. Copyright © 2009 John Wiley & Sons, Ltd.     

A novel mass spectrometry‐based method for simultaneous determination of asymmetric and symmetric dimethylarginine,l‐arginine and l‐citrulline optimized for LC‐MS‐TOF and LC‐MS/MS

Nitric oxide (NO) is a regulatory molecule involved in many biological processes. NO is produced by nitric oxide synthase by conversion of l‐ arginine to l‐ citrulline. l‐ Arginine methylated derivatives, asymmetric and symmetric dimethylarginines (asymmetric dimethylarginine, ADMA, and symmetric dimethylarginine, SDMA), regulate l‐ arginine availability and the activity of nitric oxide synthase. As such, they have been frequently investigated as potential biomarkers in pathologies associated with dysfunctions in NO synthesis. Here, we present a new multistep analytical methodology based on liquid chromatography combined with mass spectrometry for the accurate identification of l‐ arginine, l‐ citrulline, ADMA and SDMA. Compounds are measured as stable 2,3,4,5,6‐pentafluorobenzoyl chloride derivatives, which allows for simultaneous analysis of all compounds through chromatographic separation of ADMA and SDMA using a reverse‐phase column. Serum aliquots (100 μL) were spiked with isotope‐labeled internal standards and sodium carbonate buffer. The derivatization process was carried out at 25°C for 10 minu using pentafluorobenzoyl chloride as derivatization reagent. Calibration demonstrated good linearity (R ² = 0.9966–0.9986) for all derivatized compounds. Good accuracy (94.67–99.91%) and precision (1.92–11.8%) were observed for the quality control samples. The applicability of the method was evaluated in a cohort of angiological patients and healthy volunteers. The method discerned significantly lower l‐ arginine and l‐ citrulline in angiologic patients. This robust and fast LC‐ESI‐MS method may be a useful tool in quantitative analysis of l‐ arginine, ADMA, SDMA and l‐ citrulline.     

Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis

Characterizing the metabolic changes pertaining to hepatocellular carcinoma (HCC) in patients with liver cirrhosis is believed to contribute towards early detection, treatment, and understanding of the molecular mechanisms of HCC. In this study, we compare metabolite levels in sera of 78 HCC cases with 184 cirrhotic controls by using ultra performance liquid chromatography coupled with a hybrid quadrupole time-of-flight mass spectrometry (UPLC–QTOF MS). Following data preprocessing, the most relevant ions in distinguishing HCC cases from patients with cirrhosis are selected by parametric and non-parametric statistical methods. Putative metabolite identifications for these ions are obtained through mass-based database search. Verification of the identities of selected metabolites is conducted by comparing their MS/MS fragmentation patterns and retention time with those from authentic compounds. Quantitation of these metabolites is performed in a subset of the serum samples (10 HCC and 10 cirrhosis) using isotope dilution by selected reaction monitoring (SRM) on triple quadrupole linear ion trap (QqQLIT) and triple quadrupole (QqQ) mass spectrometers. The results of this analysis confirm that metabolites involved in sphingolipid metabolism and phospholipid catabolism such as sphingosine-1-phosphate (S-1-P) and lysophosphatidylcholine (lysoPC 17:0) are up-regulated in sera of HCC vs. those with liver cirrhosis. Down-regulated metabolites include those involved in bile acid biosynthesis (specifically cholesterol metabolism) such as glycochenodeoxycholic acid 3-sulfate (3-sulfo-GCDCA), glycocholic acid (GCA), glycodeoxycholic acid (GDCA), taurocholic acid (TCA), and taurochenodeoxycholate (TCDCA). These results provide useful insights into HCC biomarker discovery utilizing metabolomics as an efficient and cost-effective platform. Our work shows that metabolomic profiling is a promising tool to identify candidate metabolic biomarkers for early detection of HCC cases in high risk population of cirrhotic patients.     

Semi‐quantitative and structural metabolic phenotyping by direct infusion ion trap mass spectrometry and its application in genetical metabolomics

The identification of quantitative trait loci (QTL) for plant metabolites requires the quantitation of these metabolites across a large range of progeny. We developed a rapid metabolic profiling method using both untargeted and targeted direct infusion tandem mass spectrometry (DIMSMS) with a linear ion trap mass spectrometer yielding sufficient precision and accuracy for the quantification of a large number of metabolites in a high‐throughput environment. The untargeted DIMSMS method uses top‐down data‐dependent fragmentation yielding MS² and MS³ spectra. We have developed software tools to assess the structural homogeneity of the MS² and MS³ spectra hence their utility for phenotyping and genetical metabolomics. In addition we used a targeted DIMS(MS) method for rapid quantitation of specific compounds. This method was compared with targeted LC/MS/MS methods for these compounds. The DIMSMS methods showed sufficient precision and accuracy for QTL discovery. We phenotyped 200 individual Lolium perenne genotypes from a mapping population harvested in two consecutive years. Computational and statistical analyses identified 246 nominal m/z bins with sufficient precision and homogeneity for QTL discovery. Comparison of the data for specific metabolites obtained by DIMSMS with the results from targeted LC/MS/MS analysis showed that quantitation by this metabolic profiling method is reasonably accurate. Of the top 100 MS¹ bins, 22 ions gave one or more reproducible QTL across the 2 years. Copyright © 2009 John Wiley & Sons, Ltd.